Статті в журналах з теми "Short Read Mapping (SRM)"
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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 джерелаTran, Hong, Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools." Advances in Bioinformatics 2014 (April 15, 2014): 1–11. http://dx.doi.org/10.1155/2014/472045.
Повний текст джерелаHoutgast, Ernst Joachim, Vlad-Mihai Sima, Koen Bertels, and Zaid Al-Ars. "Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths." Computational Biology and Chemistry 75 (August 2018): 54–64. http://dx.doi.org/10.1016/j.compbiolchem.2018.03.024.
Повний текст джерелаWilton, Richard, and Alexander S. Szalay. "Performance optimization in DNA short-read alignment." Bioinformatics 38, no. 8 (February 9, 2022): 2081–87. http://dx.doi.org/10.1093/bioinformatics/btac066.
Повний текст джерелаWood, David L. A., Qinying Xu, John V. Pearson, Nicole Cloonan, and Sean M. Grimmond. "X-MATE: a flexible system for mapping short read data." Bioinformatics 27, no. 4 (January 6, 2011): 580–81. http://dx.doi.org/10.1093/bioinformatics/btq698.
Повний текст джерелаPireddu, L., S. Leo, and G. Zanetti. "SEAL: a distributed short read mapping and duplicate removal tool." Bioinformatics 27, no. 15 (June 22, 2011): 2159–60. http://dx.doi.org/10.1093/bioinformatics/btr325.
Повний текст джерелаLinheiro, Raquel, and John Archer. "Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly." F1000Research 11 (January 31, 2022): 120. http://dx.doi.org/10.12688/f1000research.108489.1.
Повний текст джерелаTewolde, Rediat, Timothy Dallman, Ulf Schaefer, Carmen L. Sheppard, Philip Ashton, Bruno Pichon, Matthew Ellington, Craig Swift, Jonathan Green, and Anthony Underwood. "MOST: a modified MLST typing tool based on short read sequencing." PeerJ 4 (August 17, 2016): e2308. http://dx.doi.org/10.7717/peerj.2308.
Повний текст джерелаHoutgast, Ernst Joachim, VladMihai Sima, Koen Bertels, and Zaid AlArs. "An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM." ACM SIGARCH Computer Architecture News 44, no. 4 (January 11, 2017): 38–43. http://dx.doi.org/10.1145/3039902.3039910.
Повний текст джерелаPorter, Jacob, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data." BMC Genomics 16, Suppl 11 (2015): S2. http://dx.doi.org/10.1186/1471-2164-16-s11-s2.
Повний текст джерелаCechova, Monika. "Probably Correct: Rescuing Repeats with Short and Long Reads." Genes 12, no. 1 (December 31, 2020): 48. http://dx.doi.org/10.3390/genes12010048.
Повний текст джерелаProdanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (October 9, 2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.
Повний текст джерелаCastells-Rufas, David, Santiago Marco-Sola, Juan Carlos Moure, Quim Aguado, and Antonio Espinosa. "FPGA Acceleration of Pre-Alignment Filters for Short Read Mapping With HLS." IEEE Access 10 (2022): 22079–100. http://dx.doi.org/10.1109/access.2022.3153032.
Повний текст джерелаPandey, Ram Vinay, and Christian Schlötterer. "DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster." PLoS ONE 8, no. 8 (August 23, 2013): e72614. http://dx.doi.org/10.1371/journal.pone.0072614.
Повний текст джерелаRuffalo, M., M. Koyuturk, S. Ray, and T. LaFramboise. "Accurate estimation of short read mapping quality for next-generation genome sequencing." Bioinformatics 28, no. 18 (September 7, 2012): i349—i355. http://dx.doi.org/10.1093/bioinformatics/bts408.
Повний текст джерелаGouil, Quentin, and Andrew Keniry. "Latest techniques to study DNA methylation." Essays in Biochemistry 63, no. 6 (November 22, 2019): 639–48. http://dx.doi.org/10.1042/ebc20190027.
Повний текст джерелаLimasset, Antoine, Jean-François Flot, and Pierre Peterlongo. "Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs." Bioinformatics 36, no. 5 (February 20, 2019): 1374–81. http://dx.doi.org/10.1093/bioinformatics/btz102.
Повний текст джерелаMarin, Maximillian, Roger Vargas, Michael Harris, Brendan Jeffrey, L. Elaine Epperson, David Durbin, Michael Strong, et al. "Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome." Bioinformatics 38, no. 7 (January 10, 2022): 1781–87. http://dx.doi.org/10.1093/bioinformatics/btac023.
Повний текст джерелаLee, Wan-Ping, Michael P. Stromberg, Alistair Ward, Chip Stewart, Erik P. Garrison, and Gabor T. Marth. "MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping." PLoS ONE 9, no. 3 (March 5, 2014): e90581. http://dx.doi.org/10.1371/journal.pone.0090581.
Повний текст джерелаSouthgate, Joel A., Matthew J. Bull, Clare M. Brown, Joanne Watkins, Sally Corden, Benjamin Southgate, Catherine Moore, and Thomas R. Connor. "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications." Bioinformatics 36, no. 6 (November 6, 2019): 1681–88. http://dx.doi.org/10.1093/bioinformatics/btz814.
Повний текст джерелаWei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, Ying-Chin Lin, Cheng-Yang Lee, Tzu-Hao Chang, Ben-Chang Shia, and Jung-Chun Lin. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform." International Journal of Molecular Sciences 21, no. 19 (September 26, 2020): 7110. http://dx.doi.org/10.3390/ijms21197110.
Повний текст джерелаFlouri, Tomas, Costas S. Iliopoulos, Solon P. Pissis, and German Tischler. "Mapping Short Reads to a Genomic Sequence with Circular Structure." International Journal of Systems Biology and Biomedical Technologies 1, no. 1 (January 2012): 26–34. http://dx.doi.org/10.4018/ijsbbt.2012010103.
Повний текст джерелаRichmond, Phillip Andrew, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, and Wyeth W. Wasserman. "Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper." PLOS Computational Biology 17, no. 3 (March 22, 2021): e1008815. http://dx.doi.org/10.1371/journal.pcbi.1008815.
Повний текст джерелаChen, Yen-Lung, Bo-Yi Chang, Chia-Hsiang Yang, and Tzi-Dar Chiueh. "A High-Throughput FPGA Accelerator for Short-Read Mapping of the Whole Human Genome." IEEE Transactions on Parallel and Distributed Systems 32, no. 6 (June 1, 2021): 1465–78. http://dx.doi.org/10.1109/tpds.2021.3051011.
Повний текст джерелаZhao, Qiong-Yi, Jacob Gratten, Restuadi Restuadi, and Xuan Li. "Mapping and differential expression analysis from short-read RNA-Seq data in model organisms." Quantitative Biology 4, no. 1 (March 2016): 22–35. http://dx.doi.org/10.1007/s40484-016-0060-7.
Повний текст джерелаAlser, Mohammed, Hasan Hassan, Hongyi Xin, Oğuz Ergin, Onur Mutlu, and Can Alkan. "GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping." Bioinformatics 33, no. 21 (May 31, 2017): 3355–63. http://dx.doi.org/10.1093/bioinformatics/btx342.
Повний текст джерелаWatson, Simon J., Matthijs R. A. Welkers, Daniel P. Depledge, Eve Coulter, Judith M. Breuer, Menno D. de Jong, and Paul Kellam. "Viral population analysis and minority-variant detection using short read next-generation sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (March 19, 2013): 20120205. http://dx.doi.org/10.1098/rstb.2012.0205.
Повний текст джерелаKim, Youngho, Munseong Kang, Ju-Hui Jeong, Dae Woong Kang, Soo Jun Park, and Jeong Seop Sim. "Reference Mapping Considering Swaps of Adjacent Bases." Applied Sciences 11, no. 11 (May 29, 2021): 5038. http://dx.doi.org/10.3390/app11115038.
Повний текст джерелаWeissensteiner, Matthias H., Andy W. C. Pang, Ignas Bunikis, Ida Höijer, Olga Vinnere-Petterson, Alexander Suh, and Jochen B. W. Wolf. "Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications." Genome Research 27, no. 5 (March 30, 2017): 697–708. http://dx.doi.org/10.1101/gr.215095.116.
Повний текст джерелаSoto, Daniela C., Colin Shew, Mira Mastoras, Joshua M. Schmidt, Ruta Sahasrabudhe, Gulhan Kaya, Aida M. Andrés, and Megan Y. Dennis. "Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing." Genes 11, no. 3 (March 4, 2020): 276. http://dx.doi.org/10.3390/genes11030276.
Повний текст джерелаFeng, Yi, Leslie Y. Beh, Wei-Jen Chang, and Laura F. Landweber. "SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping." Genome Biology and Evolution 12, no. 10 (August 13, 2020): 1711–18. http://dx.doi.org/10.1093/gbe/evaa147.
Повний текст джерелаTárraga, Joaquín, Vicente Arnau, Héctor Martínez, Raul Moreno, Diego Cazorla, José Salavert-Torres, Ignacio Blanquer-Espert, Joaquín Dopazo, and Ignacio Medina. "Acceleration of short and long DNA read mapping without loss of accuracy using suffix array." Bioinformatics 30, no. 23 (August 20, 2014): 3396–98. http://dx.doi.org/10.1093/bioinformatics/btu553.
Повний текст джерелаLee, Hayan, and Michael C. Schatz. "Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score." Bioinformatics 28, no. 16 (July 4, 2012): 2097–105. http://dx.doi.org/10.1093/bioinformatics/bts330.
Повний текст джерелаValiente-Mullor, Carlos, Beatriz Beamud, Iván Ansari, Carlos Francés-Cuesta, Neris García-González, Lorena Mejía, Paula Ruiz-Hueso, and Fernando González-Candelas. "One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads." PLOS Computational Biology 17, no. 1 (January 27, 2021): e1008678. http://dx.doi.org/10.1371/journal.pcbi.1008678.
Повний текст джерелаXie, Chao, Zhen Xuan Yeo, Marie Wong, Jason Piper, Tao Long, Ewen F. Kirkness, William H. Biggs, et al. "Fast and accurate HLA typing from short-read next-generation sequence data with xHLA." Proceedings of the National Academy of Sciences 114, no. 30 (July 3, 2017): 8059–64. http://dx.doi.org/10.1073/pnas.1707945114.
Повний текст джерелаJeske, Tim, Peter Huypens, Laura Stirm, Selina Höckele, Christine M. Wurmser, Anja Böhm, Cora Weigert, et al. "DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences." Bioinformatics 35, no. 22 (June 22, 2019): 4834–36. http://dx.doi.org/10.1093/bioinformatics/btz495.
Повний текст джерелаHamada, Michiaki, Edward Wijaya, Martin C. Frith, and Kiyoshi Asai. "Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection." Bioinformatics 27, no. 22 (October 5, 2011): 3085–92. http://dx.doi.org/10.1093/bioinformatics/btr537.
Повний текст джерелаLiu, Yuan, Yongchao Ma, Evan Salsman, Frank A. Manthey, Elias M. Elias, Xuehui Li, and Changhui Yan. "An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis." Journal of Bioinformatics and Computational Biology 17, no. 06 (December 2019): 1940012. http://dx.doi.org/10.1142/s0219720019400122.
Повний текст джерелаCoombe, Lauren, Vladimir Nikolić, Justin Chu, Inanc Birol, and René L. Warren. "ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs." Bioinformatics 36, no. 12 (April 20, 2020): 3885–87. http://dx.doi.org/10.1093/bioinformatics/btaa253.
Повний текст джерелаShen, Feichen, and Jeffrey M. Kidd. "Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2." Genes 11, no. 2 (January 29, 2020): 141. http://dx.doi.org/10.3390/genes11020141.
Повний текст джерелаSOGABE, Yoko, and Tsutomu MARUYAMA. "A Fast and Accurate FPGA System for Short Read Mapping Based on Parallel Comparison on Hash Table." IEICE Transactions on Information and Systems E100.D, no. 5 (2017): 1016–25. http://dx.doi.org/10.1587/transinf.2016edp7262.
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