Article
Computer Science, Information Systems
Igor Araujo, Carlos Natalino, Diego Cardoso
Summary: NFV advocates replacing specific-purpose hardware with general-purpose hardware to reduce costs and increase network operation flexibility. GPUs deployed in data centers can accelerate the packet processing capability of vNFs, but may introduce delays. Our framework proposes using GPUs to support vNF execution for improved throughput and reduced CPU resource usage.
COMPUTER COMMUNICATIONS
(2021)
Article
Computer Science, Theory & Methods
Bang Di, Jianhua Sun, Hao Chen, Dong Li
Summary: This article introduces a runtime software system called GMODx aimed at detecting GPU buffer overflow. GMODx is capable of detecting buffer overflow in fine-grained memory management without performance loss, and incurs only small runtime overhead in coarse-grained memory management.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2021)
Article
Computer Science, Software Engineering
Sebastian Deorowicz, Adam Gudys
Summary: Identifying genetic variants is crucial in the era of precision medicine, and Whisper 2 is a short-read-mapping software that provides high-quality indel variant calling. It is among the fastest tools available.
Article
Biochemical Research Methods
Shaohui Xie, Xiaotian He, Shan He, Zexuan Zhu
Summary: Researchers have developed a GPU-accelerated genomic sequencing data compressor called CURC, which efficiently compresses DNA data without loss. CURC achieves faster compression speed and competitive compression rate compared to other compressors.
Article
Computer Science, Software Engineering
Carlos Reano, Federico Silla
Summary: This study compared the performance of remote GPU virtualization across three generations of GPUs and showed that redesigning the rCUDA communication layer can improve performance and reduce execution time.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2021)
Article
Engineering, Geological
He Liu, Quansheng Liu, Hao Ma, Jacob Fish
Summary: This paper introduces a novel algorithm for contact detection in the three-dimensional combined finite-discrete element method, which is fully parallelized using CUDA. The efficiency and effectiveness of the algorithm have been validated through numerical tests, showing linear computation time proportional to the number of potential contact pairs regardless of element size distribution. The proposed methodology can also be applied to 2D FDEM and DEM.
INTERNATIONAL JOURNAL OF ROCK MECHANICS AND MINING SCIENCES
(2021)
Article
Computer Science, Interdisciplinary Applications
Seong Hyeon Hong, Jung-Il Shu, Junlin Ou, Yi Wang
Summary: A GPU-enabled design framework is presented to automate the global optimization process of microfluidic concentration gradient generators. The framework utilizes a physics-based component model for simulation and incorporates a genetic algorithm for optimization. The results demonstrate the potential of applying microfluidic design automation on the edge-computing platform in laboratory environments.
ENGINEERING WITH COMPUTERS
(2023)
Article
Biochemical Research Methods
Zhiwen Lu, Lu Guo, Jianhua Chen, Rongshu Wang
Summary: A large number of researchers have focused on improving the speed and reducing the cost of genome sequencing, which has made it easier for researchers to study and analyze genome data. However, storing and transmitting the vast amount of genome data generated by high-throughput sequencing technologies efficiently is a challenge for data compression researchers. This paper proposes an algorithm based on reference genome sequences to compress genome data in FASTA format. The algorithm utilizes the characteristics of suffix array (SA) and longest common prefix (LCP) array to select appropriate substrings and compress the target genome sequence.
BMC BIOINFORMATICS
(2023)
Article
Computer Science, Information Systems
David Castells-Rufas, Santiago Marco-Sola, Juan Carlos Moure, Quim Aguado, Antonio Espinosa
Summary: Pre-alignment filters are essential for reducing computational requirements in genomic sequence mapping. The latest filters are implemented using C/C++ based HLS to enhance portability and have achieved higher throughput and energy efficiency compared to other approaches.
Article
Engineering, Aerospace
Phasawee Saingyen, Sittiporn Channumsin, Suwat Sreesawet, Keerati Puttasuwan, Thanathip Limna
Summary: The increasing number of space objects poses greater risk to satellite damage and space debris generation. Conjunction assessment analysis plays a key role in evaluating collision risks, requiring fast computation for decision-making. This study investigates the performances of conjunction filters (Smart Sieve, CSieve, and CAOS-D) and develops screening filters to execute GPGPU with CUDA, comparing accuracy and computation times.
Article
Computer Science, Information Systems
Ali Abbas Zoraghchian, Mohammad Karim Sohrabi, Farzin Yaghmaee
Summary: Data mining is an essential technique for pattern extraction and information classification. Association rule mining is an important data mining technique that extracts useful rules and knowledge by considering the relationships and association of the data. Parallelizing the mining process using multiple GPUs can significantly reduce execution time and improve efficiency.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Computer Science, Theory & Methods
Yen-Lung Chen, Bo-Yi Chang, Chia-Hsiang Yang, Tzi-Dar Chiueh
Summary: This article introduces a high-throughput hardware accelerator for speeding up DNA short-read mapping, utilizing techniques such as Bloom filters and folded processing element arrays to significantly improve efficiency in CML selection and alignment algorithms.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2021)
Article
Computer Science, Interdisciplinary Applications
P. De Luca, A. Galletti, G. Giunta, L. Marcellino
Summary: Data assimilation is commonly used to improve prediction accuracy by estimating the best initial state of a system. This study focuses on the Gaussian convolution operation within the data assimilation approach, presenting an accelerated recursive filter and a new GPU-parallel implementation based on third-order recursive filter. Tests and experiments are conducted to evaluate the performance benefits.
JOURNAL OF COMPUTATIONAL SCIENCE
(2021)
Article
Biochemical Research Methods
Thomas Buechler, Jannik Olbrich, Enno Ohlebusch
Summary: The research focuses on developing graph-based models of pangenomes to improve read mapping efficiency and reduce memory requirements by encoding simple variations in the sequence.
Article
Computer Science, Information Systems
M. Ali Asan, Adnan Ozsoy
Summary: The article introduces a real-time parallel implementation of region covariance, achieving 6 times faster execution time over existing implementations. It improves the existing integral image calculation method on CUDA, reduces memory usage by 50%, achieves the fastest computation speed compared to existing solutions, and enhances the covariance matrix comparison metric by utilizing a lightweight distance metric for computation.
MULTIMEDIA TOOLS AND APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmueller, Matthias Zytnicki, Arne W. Nolte
Article
Biochemistry & Molecular Biology
Zhuwei Xu, Brian Green, Nicole Benoit, Michael Schatz, Sarah Wheelan, Brendan Cormack
MOLECULAR MICROBIOLOGY
(2020)
Article
Biochemical Research Methods
Maria Nattestad, Robert Aboukhalil, Chen-Shan Chin, Michael C. Schatz
Summary: Ribbon is a visualization tool that shows the positioning of alignments in both the reference genome and read contexts, providing an intuitive view to better understand structural variants and their supporting read evidence. It was developed to curate complex structural variant calls and determine if they are well supported by long-read evidence, using the same intuitive visualization method for genome-to-genome comparisons.
Article
Biotechnology & Applied Microbiology
Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C. Schatz
Summary: UNCALLED is an open-source mapper that rapidly matches nanopore current signals to a reference sequence, enabling purely computational targeted sequencing. It has been used to deplete known bacterial genomes from a metagenomics community and enrich other species, as well as enrich human genes associated with hereditary cancers for accurate detection of genetic variations and modifications.
NATURE BIOTECHNOLOGY
(2021)
Article
Biology
Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
Article
Biochemistry & Molecular Biology
T. Rhyker Ranallo-Benavidez, Zachary Lemmon, Sebastian Soyk, Sergey Aganezov, William J. Salerno, Rajiv C. McCoy, Zachary B. Lippman, Michael C. Schatz, Fritz J. Sedlazeck
Summary: SVCollector is a tool for selecting optimal subsets for resequencing, which analyses population-level VCF files from the 1000 Genomes Project and 3000 Rice Genomes Project to choose individuals with higher representativeness and more genetic diversity. The tool solves this optimization problem using a fast, greedy heuristic and an exact algorithm with integer linear programming, and can estimate the changes in diversity present with different numbers of samples.
Article
Biochemistry & Molecular Biology
Timour Baslan, Sam Kovaka, Fritz J. Sedlazeck, Yanming Zhang, Robert Wappel, Sha Tian, Scott W. Lowe, Sara Goodwin, Michael C. Schatz
Summary: Genome copy number is a significant source of genetic variation in health and disease, with Copy Number Alterations (CNAs) being inferred from short-read sequencing data in cancer. The emerging Nanopore sequencing technologies offer potential for broader clinical utility, while short-molecule Nanopore sequencing can improve accuracy in CNA inference by increasing sequence read yield.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Stephanie M. Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N. Bortvin, Michael C. Schatz, Rajiv C. McCoy
Summary: This study utilized advanced techniques to uncover key evolutionary events in the human genome, revealing that a specific haplotype present in certain Southeast Asian populations can be traced back to Neanderthal gene flow.
Article
Multidisciplinary Sciences
Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, Ben Langmead
Summary: Nanopore sequencing is a powerful tool for genomics, and the novel method SPUMONI uses efficient pan-genome indexes to achieve rapid and accurate targeted sequencing. Compared to traditional methods, SPUMONI is faster and has a smaller memory footprint.
Article
Biology
Chayakrit Krittanawong, Kipp W. Johnson, Edward Choi, Scott Kaplin, Eric Venner, Mullai Murugan, Zhen Wang, Benjamin S. Glicksberg, Christopher I. Amos, Michael C. Schatz, W. H. Wilson Tang
Summary: Polygenic diseases present unique challenges for diagnosis and management, but the advancements in AI and genomics offer unprecedented possibilities for personalized medicine.
Article
Evolutionary Biology
Peter D. Fields, Gus Waneka, Matthew Naish, Michael C. Schatz, Ian R. Henderson, Daniel B. Sloan
Summary: Intracellular transfers of mitochondrial DNA play a role in shaping nuclear genomes. Researchers have discovered a large nuclear insertion of mitochondrial DNA (numts) in Chromosome 2 of the model plant Arabidopsis thaliana. Using improved long-read sequencing technologies, they were able to determine the accurate sequence and structure of this numt, which is 641 kb in length. The study also found that the numt is transcriptionally inactive and has high levels of cytosine methylation.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jia He, Michael Alonge, Srividya Ramakrishnan, Matthias Benoit, Sebastian Soyk, Nathan T. Reem, Anat Hendelman, Joyce Van Eck, Michael C. Schatz, Zachary B. Lippman
Summary: The highly diverse Solanaceae family contains multiple widely studied models and crop species. This study focuses on the exploration of the diversity within the family, particularly in the genus Physalis. The researchers developed transformation and genome editing techniques in Physalis grisea and identified natural and engineered variations in floral traits. However, the study found that CRISPR-Cas9 targeted mutagenesis did not have an effect on the inflated calyx syndrome, a notable trait in the family. The study identified a mutation in an AP2-like gene causing the fusion of sepals and petals. These findings establish Physalis as a new model system in the Solanaceae family and provide insights into the factors driving the inflated calyx syndrome.
Article
Biochemical Research Methods
Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Alexis Battle, Sergey Aganezov, Michael C. C. Schatz
Summary: Jasmine and Iris, as fast and accurate tools, provide solutions for the comparison and analysis of structural variants (SVs) in a population. Jasmine outperforms six widely used comparison methods and identifies a set of high-confidence de novo SVs. Additionally, a unified callset of SVs and indels is provided for genotyping and assessing their impact on gene expression.
Editorial Material
Biochemical Research Methods
Sam Kovaka, Shujun Ou, Katharine M. Jenike, Michael C. Schatz
Summary: The year 2022 marks a significant milestone for accurate and fast long-read sequencing, offering competitive costs. This article discusses the crucial bioinformatics techniques required for empowering long reads in various applications and presents a vision for the future of long-read sequencing.
Letter
Cardiac & Cardiovascular Systems
Jennifer L. Hall, Sally Honeycutt, Nicole Gonzalez, Anne O'Donnell-Luria, Casey Overby Taylor, Laura Stevens, Anthony A. Philippakis, Michael C. Schatz
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2023)
