Статті в журналах з теми "Accurate Alignment of Short Reads"
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Asghari, Hossein, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, and Faraz Hach. "CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme." Bioinformatics 36, no. 12 (April 7, 2020): 3703–11. http://dx.doi.org/10.1093/bioinformatics/btaa232.
Повний текст джерелаKumar, Sanjeev, Suneeta Agarwal, and Ranvijay. "Fast and memory efficient approach for mapping NGS reads to a reference genome." Journal of Bioinformatics and Computational Biology 17, no. 02 (April 2019): 1950008. http://dx.doi.org/10.1142/s0219720019500082.
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 джерелаTeixeira, Andreia Sofia, Francisco Fernandes, and Alexandre P. Francisco. "SpliceTAPyR — An Efficient Method for Transcriptome Alignment." International Journal of Foundations of Computer Science 29, no. 08 (December 2018): 1297–310. http://dx.doi.org/10.1142/s0129054118430049.
Повний текст джерелаEbler, Jana, Peter Ebert, Wayne E. Clarke, Tobias Rausch, Peter A. Audano, Torsten Houwaart, Yafei Mao, et al. "Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes." Nature Genetics 54, no. 4 (April 2022): 518–25. http://dx.doi.org/10.1038/s41588-022-01043-w.
Повний текст джерелаLi, H., and R. Durbin. "Fast and accurate short read alignment with Burrows-Wheeler transform." Bioinformatics 25, no. 14 (May 18, 2009): 1754–60. http://dx.doi.org/10.1093/bioinformatics/btp324.
Повний текст джерелаMAURER-STROH, SEBASTIAN, VITHIAGARAN GUNALAN, WING-CHEONG WONG, and FRANK EISENHABER. "A SIMPLE SHORTCUT TO UNSUPERVISED ALIGNMENT-FREE PHYLOGENETIC GENOME GROUPINGS, EVEN FROM UNASSEMBLED SEQUENCING READS." Journal of Bioinformatics and Computational Biology 11, no. 06 (December 2013): 1343005. http://dx.doi.org/10.1142/s0219720013430051.
Повний текст джерелаGhoneimy, Samy, and Samir Abou El-Seoud. "A MapReduce Framework for DNA Sequencing Data Processing." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 4, no. 4 (December 30, 2016): 11. http://dx.doi.org/10.3991/ijes.v4i4.6537.
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 джерелаTeng, Carolina, Renan Weege Achjian, Jiang Chau Wang, and Fernando Josepetti Fonseca. "Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance." Applied Sciences 13, no. 7 (March 30, 2023): 4385. http://dx.doi.org/10.3390/app13074385.
Повний текст джерелаAl-Absi, Ahmed Abdulhakim, and Dae-Ki Kang. "Long Read Alignment with Parallel MapReduce Cloud Platform." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/807407.
Повний текст джерелаMarin, Wesley M., Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, and Jill A. Hollenbach. "High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING." PLOS Computational Biology 17, no. 8 (August 2, 2021): e1008904. http://dx.doi.org/10.1371/journal.pcbi.1008904.
Повний текст джерелаChen, Siyuan, Chengzhi Ren, Jingjing Zhai, Jiantao Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, and Chuang Ma. "CAFU: a Galaxy framework for exploring unmapped RNA-Seq data." Briefings in Bioinformatics 21, no. 2 (February 28, 2019): 676–86. http://dx.doi.org/10.1093/bib/bbz018.
Повний текст джерелаMukherjee, Kingshuk, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, and Christina Boucher. "Aligning optical maps to de Bruijn graphs." Bioinformatics 35, no. 18 (January 30, 2019): 3250–56. http://dx.doi.org/10.1093/bioinformatics/btz069.
Повний текст джерелаMagdy Mohamed Abdelaziz Barakat, Sherif, Roselina Sallehuddin, Siti Sophiayati Yuhaniz, Raja Farhana R. Khairuddin, and Yasir Mahmood. "Genome assembly composition of the String “ACGT” array: a review of data structure accuracy and performance challenges." PeerJ Computer Science 9 (July 13, 2023): e1180. http://dx.doi.org/10.7717/peerj-cs.1180.
Повний текст джерелаLiu, Yongchao, Bernt Popp, and Bertil Schmidt. "CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding." PLoS ONE 9, no. 1 (January 22, 2014): e86869. http://dx.doi.org/10.1371/journal.pone.0086869.
Повний текст джерелаWong, Thomas K. F., Teng Li, Louis Ranjard, Steven H. Wu, Jeet Sukumaran, and Allen G. Rodrigo. "An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes." PLOS Computational Biology 17, no. 9 (September 13, 2021): e1008949. http://dx.doi.org/10.1371/journal.pcbi.1008949.
Повний текст джерелаTello, Daniel, Juanita Gil, Cristian D. Loaiza, John J. Riascos, Nicolás Cardozo, and Jorge Duitama. "NGSEP3: accurate variant calling across species and sequencing protocols." Bioinformatics 35, no. 22 (April 25, 2019): 4716–23. http://dx.doi.org/10.1093/bioinformatics/btz275.
Повний текст джерелаChu, Wai Keung, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, and Kun Zhang. "Ultraaccurate genome sequencing and haplotyping of single human cells." Proceedings of the National Academy of Sciences 114, no. 47 (October 24, 2017): 12512–17. http://dx.doi.org/10.1073/pnas.1707609114.
Повний текст джерелаZhurbenko, Peter M., and Fedor N. Klimenko. "PhaseAll: a simple tool for read-based allele phasing." Ecological genetics 20, no. 1S (December 8, 2022): 32. http://dx.doi.org/10.17816/ecogen112363.
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 джерелаTapinos, Avraam, Bede Constantinides, My V. T. Phan, Samaneh Kouchaki, Matthew Cotten, and David L. Robertson. "The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences." Viruses 11, no. 5 (April 26, 2019): 394. http://dx.doi.org/10.3390/v11050394.
Повний текст джерелаLinard, Benjamin, Krister Swenson, and Fabio Pardi. "Rapid alignment-free phylogenetic identification of metagenomic sequences." Bioinformatics 35, no. 18 (January 29, 2019): 3303–12. http://dx.doi.org/10.1093/bioinformatics/btz068.
Повний текст джерелаAbde Aliy, Mohammed, Senbeta Bayeta, and Worku Takale. "Pacific bioscience sequence technology: Review." International Journal of Veterinary Science and Research 8, no. 1 (March 29, 2022): 027–33. http://dx.doi.org/10.17352/ijvsr.000108.
Повний текст джерелаElrick, Hillary, Jose Espejo Valle-Inclan, Katherine E. Trevers, Francesc Muyas, Rita Cascão, Angela Afonso, Cláudia C. Faria, Adrienne M. Flanagan, and Isidro Cortés-Ciriano. "Abstract LB080: SAVANA: a computational method to characterize structural variation in human cancer genomes using nanopore sequencing." Cancer Research 83, no. 8_Supplement (April 14, 2023): LB080. http://dx.doi.org/10.1158/1538-7445.am2023-lb080.
Повний текст джерелаAtshemyan, Sofi, Andranik Chavushyan, Nerses Berberian, Arthur Sahakyan, Roksana Zakharyan, and Arsen Arakelyan. "Characterization of BRCA1/2 mutations in patients with family history of breast cancer in Armenia." F1000Research 6 (January 10, 2017): 29. http://dx.doi.org/10.12688/f1000research.10434.1.
Повний текст джерелаOlawoye, Idowu B., Simon D. W. Frost, and Christian T. Happi. "The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake." PeerJ 8 (October 27, 2020): e10121. http://dx.doi.org/10.7717/peerj.10121.
Повний текст джерелаTrost, Brett, Susan Walker, Syed A. Haider, Wilson W. L. Sung, Sergio Pereira, Charly L. Phillips, Edward J. Higginbotham, et al. "Impact of DNA source on genetic variant detection from human whole-genome sequencing data." Journal of Medical Genetics 56, no. 12 (September 12, 2019): 809–17. http://dx.doi.org/10.1136/jmedgenet-2019-106281.
Повний текст джерелаGnerre, Sante, Brian Yik Tak Tsui, Tingting Jiang, Yvonne Kim, Dustin Ma, Indira Wu, Rebecca Nagy, and Han-Yu Chuang. "Abstract 1220: Accurately genotyping HLA and KIR alleles using cfDNA assay and k-mer based algorithm for immunotherapy." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1220. http://dx.doi.org/10.1158/1538-7445.am2022-1220.
Повний текст джерелаRajasagi, Mohini, Sachet A. Shukla, Edward F. Fritsch, David DeLuca, Gad Getz, Nir Hacohen, and Catherine J. Wu. "Tumor Neoantigens Are Abundant Across Cancers." Blood 122, no. 21 (November 15, 2013): 3265. http://dx.doi.org/10.1182/blood.v122.21.3265.3265.
Повний текст джерелаAu, Kin Fai, Jason G. Underwood, Lawrence Lee, and Wing Hung Wong. "Improving PacBio Long Read Accuracy by Short Read Alignment." PLoS ONE 7, no. 10 (October 4, 2012): e46679. http://dx.doi.org/10.1371/journal.pone.0046679.
Повний текст джерелаWang, Dan, Hai Xiang, Chao Ning, Hao Liu, Jian-Feng Liu, and Xingbo Zhao. "Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses." Briefings in Bioinformatics 21, no. 4 (June 14, 2019): 1368–77. http://dx.doi.org/10.1093/bib/bbz060.
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 джерелаNakabayashi, Ryo, and Shinichi Morishita. "HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C." Bioinformatics 36, no. 13 (May 5, 2020): 3966–74. http://dx.doi.org/10.1093/bioinformatics/btaa288.
Повний текст джерелаSchneeberger, Korbinian, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, and Detlef Weigel. "Simultaneous alignment of short reads against multiple genomes." Genome Biology 10, no. 9 (2009): R98. http://dx.doi.org/10.1186/gb-2009-10-9-r98.
Повний текст джерелаJi, Mingeun, Yejin Kan, Dongyeon Kim, Jaehee Jung, and Gangman Yi. "cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments." International Journal of Molecular Sciences 23, no. 19 (September 29, 2022): 11484. http://dx.doi.org/10.3390/ijms231911484.
Повний текст джерелаGuguchkin, Egor Pavlovich, and Evgeny Andreevich Karpulevich. "Modification of the short read alignment algorithm to improve the quality of the human whole genome sequencing data processing pipeline." Proceedings of the Institute for System Programming of the RAS 35, no. 2 (2023): 235–48. http://dx.doi.org/10.15514/ispras-2023-35(2)-17.
Повний текст джерелаWilton, Richard, Xin Li, Andrew P. Feinberg, and Alexander S. Szalay. "Arioc: GPU-accelerated alignment of short bisulfite-treated reads." Bioinformatics 34, no. 15 (March 15, 2018): 2673–75. http://dx.doi.org/10.1093/bioinformatics/bty167.
Повний текст джерелаZhang, Wenjing, Neng Huang, Jiantao Zheng, Xingyu Liao, Jianxin Wang, and Hong-Dong Li. "A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads." Genes 10, no. 1 (January 14, 2019): 44. http://dx.doi.org/10.3390/genes10010044.
Повний текст джерелаLim, Jing-Quan, Chandana Tennakoon, Peiyong Guan, and Wing-Kin Sung. "BatAlign: an incremental method for accurate alignment of sequencing reads." Nucleic Acids Research 43, no. 16 (July 13, 2015): e107-e107. http://dx.doi.org/10.1093/nar/gkv533.
Повний текст джерелаPACHECO BAUTISTA, D., R. CARREÑO AGUILERA, E. CORTÉS PÉREZ, M. GONZÁLEZ PÉREZ, J. J. MEDEL, M. A. ACEVEDO, and WEN YU. "NONLINEAR FM INDEX APPLICATION FOR ALIGNMENT OF SHORT DNA SEQUENCES USING RE-PARAMETRIZATION OF ALGORITHMS." Fractals 26, no. 03 (June 2018): 1850023. http://dx.doi.org/10.1142/s0218348x18500238.
Повний текст джерелаChon, 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 джерелаBao, H., H. Guo, J. Wang, R. Zhou, X. Lu, and S. Shi. "MapView: visualization of short reads alignment on a desktop computer." Bioinformatics 25, no. 12 (April 15, 2009): 1554–55. http://dx.doi.org/10.1093/bioinformatics/btp255.
Повний текст джерелаGrimm, Dominik, Jörg Hagmann, Daniel Koenig, Detlef Weigel, and Karsten Borgwardt. "Accurate indel prediction using paired-end short reads." BMC Genomics 14, no. 1 (2013): 132. http://dx.doi.org/10.1186/1471-2164-14-132.
Повний текст джерелаRumble, Stephen M., Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, and Michael Brudno. "SHRiMP: Accurate Mapping of Short Color-space Reads." PLoS Computational Biology 5, no. 5 (May 22, 2009): e1000386. http://dx.doi.org/10.1371/journal.pcbi.1000386.
Повний текст джерелаLee, E. Alice, Boram Lee, Yoonjoo Choi, Junseok Park, Adam Voshall, Eduardo Maury, Yeeok Kang, et al. "Abstract 1122: Pan-cancer analysis reveals roles of retrotransposon-fusion RNAs." Cancer Research 83, no. 7_Supplement (April 4, 2023): 1122. http://dx.doi.org/10.1158/1538-7445.am2023-1122.
Повний текст джерелаFirtina, Can, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, and Onur Mutlu. "Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm." Bioinformatics 36, no. 12 (March 13, 2020): 3669–79. http://dx.doi.org/10.1093/bioinformatics/btaa179.
Повний текст джерелаWilton, Richard, and Alexander S. Szalay. "Arioc: High-concurrency short-read alignment on multiple GPUs." PLOS Computational Biology 16, no. 11 (November 9, 2020): e1008383. http://dx.doi.org/10.1371/journal.pcbi.1008383.
Повний текст джерелаLee, Robyn S., and Marcel A. Behr. "Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis." Journal of Clinical Microbiology 54, no. 7 (April 13, 2016): 1891–95. http://dx.doi.org/10.1128/jcm.00364-16.
Повний текст джерелаZhao, Yongan, Xiaofeng Wang, and Haixu Tang. "A Secure Alignment Algorithm for Mapping Short Reads to Human Genome." Journal of Computational Biology 25, no. 6 (June 2018): 529–40. http://dx.doi.org/10.1089/cmb.2017.0094.
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