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In this paper we aim at investigating whether barcode sequence features can predict the read count ambiguities caused during PCR based next generation sequencing techniques. The methodologies we used are mutual information based motif…
Biological genomes are divided into coding and non-coding regions. Introns are non-coding parts within genes, while the remaining non-coding parts are intergenic sequences. To study the evolutionary significance of recombination inside…
Flash memory devices are winning the competition for storage density against magnetic recording devices. This outcome results from advances in physics that allow storage of more than one bit per cell, coupled with advances in signal…
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
We consider the design of regenerating codes for distributed storage systems that enjoy the property of local, exact and uncoded repair, i.e., (a) upon failure, a node can be regenerated by simply downloading packets from the surviving…
High-resolution recordings of extracellular potentials are fundamental for the study of neuronal networks, the basis of neuronal coding and transmission. Here we present an innovative method for an in vivo electrical imaging of Local Field…
Collaborative mobile edge computing (MEC) has emerged as a promising paradigm to enable low-capability edge nodes to cooperatively execute computation-intensive tasks. However, straggling edge nodes (stragglers) significantly degrade the…
In ecology it has become common to apply DNA barcoding to biological samples leading to datasets containing a large number of nucleotide sequences. The focus is then on inferring the taxonomic placement of each of these sequences by…
In this paper, we propose a new approach for building cellular automata to solve real-world segmentation problems. We design and train a cellular automaton that can successfully segment high-resolution images. We consider a colony that…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
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…
Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in…
Cell-based biosensors constitute a fundamental tool in biotechnology, and their relevance has greatly increased in recent years as a result of a surging demand for reduced animal testing and for high-throughput and cost-effective in vitro…
Image-based cell profiling aims to create informative representations of cell images. This technique is critical in drug discovery and has greatly advanced with recent improvements in computer vision. Inspired by recent developments in…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…