Добірка наукової літератури з теми "Short Read Mapping (SRM)"
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Статті в журналах з теми "Short Read Mapping (SRM)"
Chon, Alvin, and Xiaoqiu Huang. "SRAMM: Short Read Alignment Mapping Metrics." International Journal on Bioinformatics & Biosciences 11, no. 02 (June 30, 2021): 01–07. http://dx.doi.org/10.5121/ijbb.2021.11201.
Повний текст джерелаCline, Eliot, Nuttachat Wisittipanit, Tossapon Boongoen, Ekachai Chukeatirote, Darush Struss, and Anant Eungwanichayapant. "Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data." PeerJ 8 (December 7, 2020): e10501. http://dx.doi.org/10.7717/peerj.10501.
Повний текст джерелаYang, Xiaohong, Yue Li, Yu Wei, Zhanlong Chen, and Peng Xie. "Water Body Extraction from Sentinel-3 Image with Multiscale Spatiotemporal Super-Resolution Mapping." Water 12, no. 9 (September 17, 2020): 2605. http://dx.doi.org/10.3390/w12092605.
Повний текст джерелаCanzar, Stefan, and Steven L. Salzberg. "Short Read Mapping: An Algorithmic Tour." Proceedings of the IEEE 105, no. 3 (March 2017): 436–58. http://dx.doi.org/10.1109/jproc.2015.2455551.
Повний текст джерелаDeorowicz, Sebastian, and Adam Gudyś. "Whisper 2: Indel-sensitive short read mapping." SoftwareX 14 (June 2021): 100692. http://dx.doi.org/10.1016/j.softx.2021.100692.
Повний текст джерелаDavid, Matei, Misko Dzamba, Dan Lister, Lucian Ilie, and Michael Brudno. "SHRiMP2: Sensitive yet Practical Short Read Mapping." Bioinformatics 27, no. 7 (January 28, 2011): 1011–12. http://dx.doi.org/10.1093/bioinformatics/btr046.
Повний текст джерелаSmith, A. D., W. Y. Chung, E. Hodges, J. Kendall, G. Hannon, J. Hicks, Z. Xuan, and M. Q. Zhang. "Updates to the RMAP short-read mapping software." Bioinformatics 25, no. 21 (September 7, 2009): 2841–42. http://dx.doi.org/10.1093/bioinformatics/btp533.
Повний текст джерелаGao, Lei, Cong Wu, and Lin Liu. "AUSPP: A universal short-read pre-processing package." Journal of Bioinformatics and Computational Biology 17, no. 06 (December 2019): 1950037. http://dx.doi.org/10.1142/s0219720019500379.
Повний текст джерелаHach, Faraz, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E. Eichler, and S. Cenk Sahinalp. "mrsFAST: a cache-oblivious algorithm for short-read mapping." Nature Methods 7, no. 8 (August 2010): 576–77. http://dx.doi.org/10.1038/nmeth0810-576.
Повний текст джерелаMartinez, Hector, Joaquin Tarraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquin Dopazo, and Enrique S. Quintana-Orti. "Concurrent and Accurate Short Read Mapping on Multicore Processors." IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, no. 5 (September 1, 2015): 995–1007. http://dx.doi.org/10.1109/tcbb.2015.2392077.
Повний текст джерелаДисертації з теми "Short Read Mapping (SRM)"
Porter, Jacob Stuart. "Mapping Bisulfite-Treated Short DNA Reads." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/82870.
Повний текст джерелаPh. D.
Chacon, de San Baldomero Alejandro. "Read mapping on heterogeneous systems: scalability strategies for bioinformatic primitives." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/671736.
Повний текст джерелаLa secuenciación genómica es un componente clave en nuevos avances en medicina, y su democratización es un paso importante hacia la accesibilidad para el paciente. Los beneficios implícitos en el descubrimiento de nuevas variantes genéticas son muy amplios, incluyendo desde la detección precoz de cáncer como la medicina personalizada, pasando por el diseño de fármaco y la edición genómica. Estos usos potenciales han incrementado exponencialmente el interés de la comunidad científica en el campo de la bioinformática durante los últimos años. Además, el surgimiento de los métodos de Secuenciación de Nueva Generación ha contribuido a la reducción rápida de los costes de secuenciación, permitiendo el desarrollo de nuevas aplicaciones genómicas. El principal objetivo de esta tesis es el de mejorar el rendimiento y precisión del estado del arte de la secuenciación genética a través del uso de plataformas de computo heterogéneo y sistemas de hardware híbridos. Más específicamente, el trabajo se ha centrado en la aceleración del problema del short-read mapping, dado que se describe como uno de los estadíos del pipeline con un mayor coste computacional. De forma global, se aspiraba a reducir el tiempo de procesado y el coste de la secuenciación genética, incrementando su disponibilidad. La principal contribución de esta tesis es la integración GPU del mapper GEM3 (GEM3-GPU). Este mapper reporta los mismos datos de salida para CPU y GPU, y es uno de los primeros mappers GPU que permite el alineamiento de reads largos y variables. Las propuestas han sido validadas utilizando datos reales, dado que el mapper ha estado corriendo en producción en un centro de secuenciación (Centro Nacional de Análisis Genómico (CNAG)). En conjunción con el mapper GEM3-GPU, durante esta tesis se ha creado una librería bioinformática en CUDA (GEM-cutter). La librería provee bloques de primitivas GPU básicas que han sido altamente optimizadas. Gem-cutter ofrece una API basada en primitivas de send and receive (message passing), e incorpora un scheduler para balancear el trabajo. Además, la librería soporta todas las arquitecturas GPU y Multi-GPU.
Genomic sequencing is the key component of new advances in medicine, and its democratization is an important step in improving accessibility for the patient. The benefits involved in discovering new genomic variations are vast and include everything from early cancer detection to personalized medicine, drug design and genome editing. All of these potential uses have greatly increased the interest of the scientific community in the field of bioinformatics in recent years. Moreover, the emergence of next-generation sequencing methods has contributed to the rapid reduction of sequencing costs, enabling new applications of genomics in precision medicine. The main goal of this thesis is to improve the state of the art in performance and accuracy for genome sequencing through the use of heterogeneous computing platforms and hybrid hardware systems. More specifically, the work is focused on accelerating the problem of short-read mapping, as it is described as one of the most computationally expensive parts of the pipeline process. Overall, we aim to reduce the processing time and cost of genome sequencing, and then increasing the availability of this type analysis. The main contribution of this thesis is the full GPU integration of the GEM3 mapper (GEM3-GPU), reporting significant improvements in performance and competitive accuracy results. The mapper reports the same output files for CPU and GPU and is one of the first GPU mappers to allow very long and variable read alignment. The proposals have been validated using real data, since the mapper has been running in production at a genomic sequencing center (Centro Nacional de Análisis Genómico (CNAG)). Together with the GEM3-GPU mapper, a complete bioinformatics CUDA library (GEM-cutter) has been created. The library provides the basic building blocks for genomic applications, which are highly optimised to run on GPUs. Gem-cutter offers an API based on send and receive primitives (message passing) and incorporates a scheduler to balance the work. Furthermore, the library supports all GPU architectures and Multi-GPU execution.
Universitat Autònoma de Barcelona. Programa de Doctorat en Informàtica
Частини книг з теми "Short Read Mapping (SRM)"
Ribeca, Paolo. "Short-Read Mapping." In Bioinformatics for High Throughput Sequencing, 107–25. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4614-0782-9_7.
Повний текст джерелаZhou, Xueya, Suying Bao, Binbin Wang, Xuegong Zhang, and You-Qiang Song. "Short Read Mapping for Exome Sequencing." In Methods in Molecular Biology, 93–111. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-514-9_6.
Повний текст джерелаMenzel, Peter, Jes Frellsen, Mireya Plass, Simon H. Rasmussen, and Anders Krogh. "On the Accuracy of Short Read Mapping." In Methods in Molecular Biology, 39–59. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-514-9_3.
Повний текст джерелаMorshedi, Mostafa, and Hamid Noori. "FPGA Implementation of a Short Read Mapping Accelerator." In Lecture Notes in Computer Science, 289–96. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-56258-2_25.
Повний текст джерелаMäkinen, Veli, Niko Välimäki, Antti Laaksonen, and Riku Katainen. "Unified View of Backward Backtracking in Short Read Mapping." In Algorithms and Applications, 182–95. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12476-1_13.
Повний текст джерелаKimura, Kouichi, Asako Koike, and Kenta Nakai. "Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping." In Lecture Notes in Computer Science, 151–62. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23038-7_14.
Повний текст джерелаBhatia, Dinesh, and Animesh Mishra. "A Novel Artificial Intelligence Technique for Analysis of Real-Time Electro-Cardiogram Signal for the Prediction of Early Cardiac Ailment Onset." In Handbook of Research on Advancements of Artificial Intelligence in Healthcare Engineering, 42–66. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-2120-5.ch003.
Повний текст джерелаFox, Heather A. "Mapping Spatial Consciousness in Kate Chopin’S Bayou Folk (1894)." In Arranging Stories, 19–56. University Press of Mississippi, 2022. http://dx.doi.org/10.14325/mississippi/9781496840516.003.0002.
Повний текст джерелаJ. Espona, Maria. "Interdisciplinary Integrated Tools to Problem Solving 2.0." In Contemporary Issues in Information Systems - A Global Perspective. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.101456.
Повний текст джерелаFiore, Teresa. "All at One Point: The Unlikely Connections between Italy’s Emigration, Immigration, and (Post)Colonialism." In Pre-Occupied Spaces. Fordham University Press, 2017. http://dx.doi.org/10.5422/fordham/9780823274321.003.0001.
Повний текст джерелаТези доповідей конференцій з теми "Short Read Mapping (SRM)"
Olson, Corey B., Maria Kim, Cooper Clauson, Boris Kogon, Carl Ebeling, Scott Hauck, and Walter L. Ruzzo. "Hardware Acceleration of Short Read Mapping." In 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2012. http://dx.doi.org/10.1109/fccm.2012.36.
Повний текст джерелаArram, James, Kuen Hung Tsoi, Wayne Luk, and Peiyong Jiang. "Reconfigurable Acceleration of Short Read Mapping." In 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2013. http://dx.doi.org/10.1109/fccm.2013.57.
Повний текст джерелаDai, Dong, Xi Li, Chao Wang, and Xuehai Zhou. "Cloud Based Short Read Mapping Service." In 2012 IEEE International Conference on Cluster Computing (CLUSTER). IEEE, 2012. http://dx.doi.org/10.1109/cluster.2012.60.
Повний текст джерелаChen, Yupeng, Bertil Schmidt, and Douglas L. Maksell. "An FPGA aligner for short read mapping." In 2012 22nd International Conference on Field Programmable Logic and Applications (FPL). IEEE, 2012. http://dx.doi.org/10.1109/fpl.2012.6339267.
Повний текст джерелаAji, Ashwin M., Liqing Zhang, and Wu-chun Feng. "GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors." In 2010 IEEE 13th International Conference on Computational Science and Engineering (CSE). IEEE, 2010. http://dx.doi.org/10.1109/cse.2010.29.
Повний текст джерелаSogabe, Yoko, and Tsutomu Maruyama. "An acceleration method of short read mapping using FPGA." In 2013 International Conference on Field-Programmable Technology (FPT). IEEE, 2013. http://dx.doi.org/10.1109/fpt.2013.6718385.
Повний текст джерелаChen, Yupeng, Bertil Schmidt, and Douglas Leslie Maskell. "Accelerating short read mapping on an FPGA (abstract only)." In the ACM/SIGDA international symposium. New York, New York, USA: ACM Press, 2012. http://dx.doi.org/10.1145/2145694.2145740.
Повний текст джерелаNg, Ho-Cheung, Izaak Coleman, Shuanglong Liu, and Wayne Luk. "Reconfigurable Acceleration of Short Read Mapping with Biological Consideration." In FPGA '21: The 2021 ACM/SIGDA International Symposium on Field Programmable Gate Arrays. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3431920.3439280.
Повний текст джерелаPreuber, Thomas B., Oliver Knodel, and Rainer G. Spallek. "Short-Read Mapping by a Systolic Custom FPGA Computation." In 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2012. http://dx.doi.org/10.1109/fccm.2012.37.
Повний текст джерелаKnodel, Oliver, Thomas B. Preusser, and Rainer G. Spallek. "Next-generation massively parallel short-read mapping on FPGAs." In 2011 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP). IEEE, 2011. http://dx.doi.org/10.1109/asap.2011.6043268.
Повний текст джерелаЗвіти організацій з теми "Short Read Mapping (SRM)"
Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.
Повний текст джерела