Related papers: GenStore: A High-Performance and Energy-Efficient …
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Recent excitement in the database community surrounding new applications?analytic, scientific, graph, geospatial, etc.?has led to an explosion in research on database storage systems. New storage systems are vital to the database community,…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
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]…
Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In-memory ordered key-value stores are an important building block in modern distributed applications. We present Honeycomb, a hybrid software-hardware system for accelerating read-dominated workloads on ordered key-value stores that…
Linearizable datastores are desirable because they provide users with the illusion that the datastore is run on a single machine that performs client operations one at a time. To reduce the performance cost of providing this illusion, many…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
RDMA (Remote Direct Memory Access) is widely exploited in building key-value stores to achieve ultra low latency. In RDMA-based key-value stores, the indexing time takes a large fraction (up to 74%) of the overall operation latency as RDMA…
Background: Identifying all possible mapping locations of next-generation sequencing (NGS) reads is highly essential in several applications such as prediction of genomic variants or protein binding motifs located in repeat regions, isoform…
Sorting is a fundamental operation across numerous computational domains. Traditionally, this process involves transferring data from main memory to a processing unit for sorting, followed by writing the sorted data back to memory. This…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
Genetic Programming (GP) is known to suffer from the burden of being computationally expensive by design. While, over the years, many techniques have been developed to mitigate this issue, data vectorization, in particular, is arguably…