Search Results - High-performance computing in bioinformatics

A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening by Gorgulla, Christoph, Padmanabha Das, Krishna M., Leigh, Kendra E., Cespugli, Marco, Fischer, Patrick D., Wang, Zi-Fu, Tesseyre, Guilhem, Pandita, Shreya, Shnapir, Alec, Calderaio, Anthony, Gechev, Minko, Rose, Alexander, Lewis, Noam, Hutcheson, Colin, Yaffe, Erez, Luxenburg, Roni, Herce, Henry D., Durmaz, Vedat, Halazonetis, Thanos D., Fackeldey, Konstantin, Patten, J.J., Chuprina, Alexander, Dziuba, Igor, Plekhova, Alla, Moroz, Yurii, Radchenko, Dmytro, Tarkhanova, Olga, Yavnyuk, Irina, Gruber, Christian, Yust, Ryan, Payne, Dave, Näär, Anders M., Namchuk, Mark N., Davey, Robert A., Wagner, Gerhard, Kinney, Jamie, Arthanari, Haribabu

“…The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted…”
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BOA: A partitioned view of genome assembly by An, Xiaojing, Ghosh, Priyanka, Keppler, Patrick, Kurt, Sureyya Emre, Krishnamoorthy, Sriram, Sadayappan, Ponnuswamy, Rajam, Aravind Sukumaran, Çatalyürek, Ümit V., Kalyanaraman, Ananth

“…De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA…”
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Donor-acceptor-type poly[chalcogenoviologen-alt-triphenylamine] for synaptic biomimicking and neuromorphic computing by Zhao, Zhizheng, Che, Qiang, Wang, Kexin, El-Khouly, Mohamed E., Liu, Jiaxuan, Fu, Yubin, Zhang, Bin, Chen, Yu

“…Polymer memristors are preeminent candidates for low-power edge computing paradigms…”
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Teaching computational genomics and bioinformatics on a high performance computing cluster—a primer by Sethuraman, Arun

“… However, with increased availability of resources such as NSF XSEDE, Google Cloud, Amazon AWS, and other high-performance computing (HPC…”
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Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences by Seiler, Enrico, Mehringer, Svenja, Darvish, Mitra, Turc, Etienne, Reinert, Knut

“… Our data structure can be used to accelerate various core bioinformatics applications. We show this by re-implementing the distributed read mapping tool DREAM-Yara. [Display omitted…”
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The backpack quotient filter: A dynamic and space-efficient data structure for querying k-mers with abundance by Levallois, Victor, Andreace, Francesco, Le Gal, Bertrand, Dufresne, Yoann, Peterlongo, Pierre

“…Genomic data sequencing is crucial for understanding biological systems. As genomic databases like the European Nucleotide Archive expand exponentially,…”
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XDec-CHI reveals immunosuppressive interactions in pancreatic ductal adenocarcinoma by LaPlante, Emily L., Liu, Dongliang, Petrosyan, Varduhi, Yao, Qizhi, Milosavljevic, Aleksandar

“…Most cancers harbor a diverse collection of cell types including a typically heterogeneous cancer cell fraction. To reconstruct cell-intrinsic and heterotypic…”
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Dynamic partitioning of search patterns for approximate pattern matching using search schemes by Renders, Luca, Marchal, Kathleen, Fostier, Jan

“…Search schemes constitute a flexible and generic framework to describe how all approximate occurrences of a search pattern in a text can be found efficiently…”
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Biclustering in bioinformatics using big data and High Performance Computing applications: challenges and perspectives, a review: Biclustering in bioinformatics using Big Data and High by López-Fernández, Aurelio, Gomez-Vela, Francisco A., Rodriguez-Baena, Domingo S., Delgado-Chaves, Fernando M., Gonzalez-Dominguez, Jorge

“… This review aims to examine how biclustering methods and their validation strategies are evolving to meet the demands of High Performance Computing (HPC…”
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Bioinformatics and High-Performance Computing Methods for Deciphering and Fighting COVID-19—Editorial by Cannataro, Mario, Agapito, Giuseppe

“…The COVID-19 disease (Coronavirus Disease 19), caused by the SARS-CoV-2 virus (Severe Acute Respiratory Syndrome Coronavirus 2), has posed many challenges…”
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bioScience: A new python science library for high-performance computing bioinformatics analytics by López-Fernández, Aurelio, Gómez-Vela, Francisco A., Gonzalez-Dominguez, Jorge, Bidare-Divakarachari, Parameshachari

“…BioScience is an advanced Python library designed to satisfy the growing data analysis needs in the field of bioinformatics by leveraging High-Performance Computing (HPC…”
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Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters by Cheng, Trinity, Chin, Pei-Ju, Cha, Kenny, Petrick, Nicholas, Mikailov, Mike

“… The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters…”
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Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters by Cheng, Trinity, Chin, Pei-Ju, Cha, Kenny, Petrick, Nicholas, Mikailov, Mike

“… The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters…”
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Manycore High-Performance Computing in Bioinformatics by Varré, Jean-Stéphane, Schmidt, Bertil, Janot, Stéphane, Giraud, Mathieu

“…) are a first step towards massively multicore processors. They allow everyone to have some teraflops of cheap computing power in a personal computer. The CUDA library (released in 2007…”
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ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community by Castrignanò, Tiziana, Gioiosa, Silvia, Flati, Tiziano, Cestari, Mirko, Picardi, Ernesto, Chiara, Matteo, Fratelli, Maddalena, Amente, Stefano, Cirilli, Marco, Tangaro, Marco Antonio, Chillemi, Giovanni, Pesole, Graziano, Zambelli, Federico

“… For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians…”
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Parallel computing in bioinformatics: a view from high-performance, heterogeneous, and cloud computing by Vega-Rodríguez, Miguel A., Santander-Jiménez, Sergio

“… This special issue brings together high-quality state-of-the-art contributions about parallel computing in bioinformatics, from different points of view or perspectives, that is, from high…”
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High-performance computing service for bioinformatics and data science by Courneya, Jean-Paul, Mayo, Alexa

“… In this innovative project, the library supports analysis of high-throughput data from global molecular profiling experiments by offering a high-performance computer with open source software along…”
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Workflow optimization of performance and quality of service for bioinformatics application in high performance computing by Al-Ali, Rashid, Kathiresan, Nagarajan, Anbari, Mohammed El, Schendel, Eric R., Zaid, Tariq Abu

“… Nowadays, High Performance Computing (HPC) systems commonly used in bioinformatics, such as genome sequencing, incorporate multi-processor architectures…”
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Biclustering in bioinformatics using big data and High Performance Computing applications: challenges and perspectives, a review by López-Fernández, Aurelio, Gomez-Vela, Francisco A., Rodriguez-Baena, Domingo S., Delgado-Chaves, Fernando M., Gonzalez-Dominguez, Jorge

“… This review aims to examine how biclustering methods and their validation strategies are evolving to meet the demands of High Performance Computing (HPC…”
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BioinfoPortal: A scientific gateway for integrating bioinformatics applications on the Brazilian national high-performance computing network by Ocaña, Kary A.C.S., Galheigo, Marcelo, Osthoff, Carla, Gadelha, Luiz M.R., Porto, Fabio, Gomes, Antônio Tadeu A., de Oliveira, Daniel, Vasconcelos, Ana Tereza

“… Bioinformatics covers a wide range of important applications in health, diversity, and life sciences with the understanding of the high-performance computing culture to accelerate the transition…”
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