A survey of sequence alignment algorithms for next-generation sequencing

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Items 301–400 of 876

1. Approximate string matching for high-throughput sequencing
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3. Cardiovascular Transcriptomics and Epigenomics Using Next-Generation Sequencing
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4. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola
   Kirill A. Grigorev, Sergei F. Kliver, Pavel V. Dobrynin, Aleksey S. Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Adam L. Brandt, Liz A. Paulino, Rosanna Carreras‐De León et al. · 2018 · GigaScience
5. Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis
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7. When less is more: sketching with minimizers in genomics
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8. Towards next generation CHO cell biology: Bioinformatics methods for RNA‐Seq‐based expression profiling
   Craig Monger, Paul S. Kelly, Clair Gallagher, MARTIN M. CLYNES, Niall Barron, Colin Clarke · 2015 · Biotechnology Journal
9. An Adaptive Workflow Scheduling Scheme Based on an Estimated Data Processing Rate for Next Generation Sequencing in Cloud Computing
   Byungsang Kim, Chan‐Hyun Youn, Yong-Sung Park, Yonggyu Lee, Wan Choi · 2012 · Journal of Information Processing Systems
10. Parallel architecture for DNA sequence inexact matching with Burrows-Wheeler Transform
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11. POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
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12. Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data
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13. The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools
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14. lobSTR: A Short Tandem Repeat Profiler for Personal Genomes
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15. The Promise and Practicality of Population Genomics Research with Endangered Species
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16. Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes
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17. Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression
    Shuai Yuan, Zhaohui Steve Qin · 2012 · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
18. Re-alignment of the unmapped reads with base quality score
    Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li, Yi Feng Pan · 2015 · BMC Bioinformatics
19. Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques
    Francisco Manuel Ortuño, Olga Valenzuela, H. Pomares, Fernando Rojas, Javier Pérez-Florido, José Urquiza, Ignacio Rojas · 2012 · Nucleic Acids Research
20. A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis
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21. Predictive Data Delivery to Mobile Users Through Mobility Learning in Wireless Sensor Networks
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22. Pipeliner: software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing
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23. Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data
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24. SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition
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25. Enabling fast and energy-efficient FM-index exact matching using processing-near-memory
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26. Cardiovascular Genomics: A Biomarker Identification Pipeline
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27. High-throughput sequencing in veterinary infection biology and diagnostics
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28. DNA Sequence Motif
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29. PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data
    Wei Shao, Mary F. Kearney, Valerie F. Boltz, Jonathan Spindler, John W. Mellors, Frank M. Maldarelli, John M. Coffin · 2014 · Journal of Virological Methods
30. Tecnologías de secuenciación de nueva generación en diagnóstico genético pre- y postnatal
    Benjamín Rodríguez‐Santiago, Lluı́s Armengol · 2012 · Diagnóstico Prenatal
31. A fast read alignment method based on seed-and-vote for next generation sequencing
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32. Mapping Short Sequence Reads to a Reference Genome
    Jui‐Hung Hung, Zhiping Weng · 2016 · Cold Spring Harbor Protocols
33. Cohort Representation and Exploration
    Behrooz Omidvar-Tehrani, Sihem Amer-Yahia, Laks V. S. Lakshmanan · 2018 · IEEE International Conference on Data Science and Advanced Analytics (DSAA)
34. GenoDedup: Similarity-Based Deduplication and Delta-Encoding for Genome Sequencing Data
    Vinicius V. Cogo, João T. Paulo, Alysson Bessani · 2020 · IEEE Transactions on Computers
35. One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
    Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi‐Juan Hu, Zhaohui Steve Qin · 2015 · PLoS Computational Biology
36. Germline correction of an epimutation related to Silver-Russell syndrome
    Céline Bruno, Virginie Carmignac, Irène Netchine, Cécile Choux, Yannis Duffourd, Laurence Olivier Faivre, Christel Thauvin‐Robinet, Yves Le Bouc, Paul Sagot, Déborah Bourc’his et al. · 2015 · Human Molecular Genetics
37. MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data
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38. The distribution of cycles in breakpoint graphs of signed permutations
    Simona Grusea, Anthony Labarre · 2013 · Discrete Applied Mathematics
39. The impact of RNA-seq aligners on gene expression estimation
    Cheng Yang, Po-Yen Wu, Tong Li, John H. Phan, May Dongmei Wang · 2015 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
40. Workflow optimization of performance and quality of service for bioinformatics application in high performance computing
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41. Fully-sensitive seed finding in sequence graphs using a hybrid index
    Ali Ghaffaari, Tobias Marschall · 2019 · Bioinformatics
42. Genetic Profiling for Risk Reduction in Human Cardiovascular Disease
    Megan J. Puckelwartz, Elizabeth M. McNally · 2014 · Genes
43. DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation
    Beat Wolf, Pierre Kuonen, Thomas Dandekar, David Atlan · 2015 · BioMed Research International
44. Reducing False-Positive Incidental Findings with Ensemble Genotyping and Logistic Regression Based Variant Filtering Methods
    Kyu‐Baek Hwang, In‐Hee Lee, Jin‐Ho Park, Tina M. Hambuch, Yongjoon Choe, Minhyeok Kim, Kyungjoon Lee, Taemin Song, Matthew B. Neu, Neha Gupta et al. · 2014 · Human Mutation
45. How genome complexity can explain the difficulty of aligning reads to genomes
    Vinhthuy Phan, Shanshan Gao, Quang Tran, Nam S. Vo · 2015 · BMC Bioinformatics
46. A review of alignment based similarity measures for web usage mining
    Vinh-Trung Luu, Germain Forestier, Jonathan Weber, Paul Bourgeois, Fahima Djelil, Pierre-Alain Müller · 2019 · Artificial Intelligence Review
47. Large-Scale DNA Sequence Analysis in the Cloud: A Stream-Based Approach
    Romeo Kienzler, Rémy Bruggmann, Anand Ranganathan, Nesime Tatbul · 2012 · Lecture notes in computer science
48. Candida and Candidiasis
    Tülin Aşkun · 2022 · IntechOpen eBooks
49. GenArchBench: A genomics benchmark suite for arm HPC processors
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50. RNA-Seq reveals differentially expressed isoforms and novel splice variants in buccal mucosal cancer
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51. Smith-Waterman algorithm on heterogeneous systems: A case study
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52. Missing genetic risk in neural tube defects: Can exome sequencing yield an insight?
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53. RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants
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54. Unbiased Taxonomic Annotation of Metagenomic Samples
    Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente · 2017 · Journal of Computational Biology
55. An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites
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56. Accelerating Sequence-to-Graph Alignment on Heterogeneous Processors
    Zonghao Feng, Qiong Luo · 2021 · Proceedings of the International Conference on Parallel Processing
57. Performance improvement of BWA MEM algorithm using data-parallel with concurrent parallelization
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58. Deep sequencing of small RNAs in plants: applied bioinformatics
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59. Implementation of Smith-Waterman Algorithm in OpenCL for GPUs
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60. BIIIA: a bioinformatics-inspired image identification approach
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61. Exploring Frequented Regions in Pan-Genomic Graphs
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62. DNA AS X: An Information-Coding-Based Model to Improve the Sensitivity in Comparative Gene Analysis
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63. sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping
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64. CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model
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65. A Long Fragment Aligner called ALFALFA
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66. Sequencing Human Mitochondrial Hypervariable Region II as a Molecular Fingerprint for Environmental Waters
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67. A performance comparison of data and memory allocation strategies for sequence aligners on NUMA architectures
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68. Identification of missing variants by combining multiple analytic pipelines
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69. Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor
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70. Can whole-exome sequencing data be used for linkage analysis?
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71. Sequence Alignment Tools: One Parallel Pattern to Rule Them All?
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72. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function
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73. Approximate String Matching Using a Bidirectional Index
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74. Accelerating large-scale genomic analysis with Spark
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75. Large-scale screening of circulating microRNAs in individuals with HIV-1 mono-infections reveals specific liver damage signatures
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76. mBWA: A Massively Parallel Sequence Reads Aligner
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77. Neural network based cloud computing platform for bioinformatics
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78. CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms
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79. User-assisted alignment of Arabic historical manuscripts
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80. Applications of second generation sequencing technologies in complex disorders.
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81. The impact of quality filter for RNA-Seq
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82. An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
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83. Genomic Technologies in Medicine and Health
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84. SMEM++: A Pipelined and Time-Multiplexed SMEM Seeding Accelerator for Genome Sequencing
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85. Privately computing set-maximal matches in genomic data
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86. Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform
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87. A Framework to Design and Implement Real-time Multicore Schedulers using Machine Learning
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88. Biobanking and genetic markers for parasites in fish stock studies
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89. Tentacle: distributed quantification of genes in metagenomes
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90. 2D shape recognition using biological sequence alignment tools
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91. Sequence Alignment Algorithms for Intrusion Detection in the Internet of Things
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92. Versa: A 36-Core Systolic Multiprocessor With Dynamically Reconfigurable Interconnect and Memory
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93. Analysis methods for the gut microbiome in neuropsychiatric and neurodegenerative disorders
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94. Porting and Optimizing BWA-MEM2 Using the Fujitsu A64FX Processor
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95. A Multi-Objective Evolutionary Algorithm for Improving Multiple Sequence Alignments
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96. Negative regulation of miRNA sorting into EVs is mediated by the capacity of RBP PCBP2 to impair the SYNCRIP-dependent miRNA loading
    Francesco Marocco, Sabrina Garbo, Claudia Montaldo, Alessio Colantoni, Luca Quattrocchi, Gioele Gaboardi, Giovanna Sabarese, Carla Cicchini, Mario Lecce, Alessia Carnevale et al. · 2025 · eLife
97. Challenges in exome analysis by LifeScope and its alternative computational pipelines
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98. Big data from small samples: Informatics of next‐generation sequencing in cytopathology
    Sinchita Roy‐Chowdhuri, Somak Roy, Sara E. Monaco, Mark J. Routbort, Liron Pantanowitz · 2016 · Cancer Cytopathology
99. Is the trophosome of Ridgeia piscesae monoclonal?
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100. A High-Performance Genomic Accelerator for Accurate Sequence-to-Graph Alignment Using Dynamic Programming Algorithm
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