Related papers: Read Mapping Near Non-Volatile Memory
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…
Next-generation sequencing (NGS) to profile temporal changes in living systems is gaining more attention for deriving better insights into the underlying biological mechanisms compared to traditional static sequencing experiments.…
Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…
Approximate nearest neighbor search (ANNS) is a key retrieval technique for vector database and many data center applications, such as person re-identification and recommendation systems. It is also fundamental to retrieval augmented…
As transistor-based memory technologies like dynamic random access memory (DRAM) approach their scalability limits, the need to explore alternative storage solutions becomes increasingly urgent. Phase-change memory (PCM) has gained…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
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…
Hand-sized Deoxyribonucleic acid (DNA) sequencing machines are of growing importance in several life sciences fields as their small footprints enable a broader range of use cases than their larger, stationary counterparts. However, as…
In unforeseen situations, such as nuclear power plant's or civilian radiation accidents, there is a need for effective and computationally inexpensive methods to determine the expression level of a selected gene panel, allowing for rough…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
The practical NAND flash memory suffers from various non-stationary noises that are difficult to be predicted. Furthermore, the data retention noise induced channel offset is unknown during the readback process. This severely affects the…
Human cancers present a significant public health challenge and require the discovery of novel drugs through translational research. Transcriptomics profiling data that describes molecular activities in tumors and cancer cell lines are…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
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…
Non-volatile memory (NVM) technologies such as spin-transfer torque magnetic random access memory (STT-MRAM) and spin-orbit torque magnetic random access memory (SOT-MRAM) have significant advantages compared to conventional SRAM due to…