A survey of sequence alignment algorithms for next-generation sequencing

Li, H., Homer, N.·2010·Briefings in Bioinformatics

Cited by (876)

Items 801–876 of 876

  1. Plant virus identification and virus-vector-host interactions
    Yahya Z. A. Gaafar · 2019
  2. Summarizing Diverging String Sequences, with Applications to Chain-Letter Petitions
    Patty Commins, David Liben‐Nowell, Tina Liu, Kiran Tomlinson · 2020 · arXiv (Cornell University)
  3. Whole-exome capture and next-generation sequencing to discover rare variants predisposing to congenital heart disease
    Matthieu J. Miossec · 2016
  4. Enabling large-scale dataset analysis in resource-constrained environments through application-aware preprocessing
    Jack Parry · 2020 · Queensland University of Technology
  5. PANDA: Processing-in-MRAM Accelerated De Bruijn Graph based DNA Assembly
    Shaahin Angizi, Naima Ahmed Fahmi, Wei Zhang, Deliang Fan · 2020 · arXiv (Cornell University)
  6. Analysis of Short-read Aligners using Genome Sequence Complexity
    Quang Tran, Nam S. Vo, Eric Hicks, Tin Nguyen, Vinhthuy Phan · 2020 · International Conference on Knowledge and Systems Engineering/Proceedings
  7. Authors and Affiliations 3
    Nick Parkinson, Siarhei Maslau, Ben Ferneyhough, Gang Zhang, Lorna Gregory, David Buck, Jiannis Ragoussis, Chris Paul Ponting, Michael D. Fischer, Cranmer Terrace · 2011
  8. Fundamentos y aplicaciones biomédicas de las principales tecnologías de secuenciación: una revisión de literatura
    Anny Camargo, Karen Nattaly Valero González, Alida Marcela Gómez Rodríguez, Diego Fernando Camargo Mancipe, Carlos Fernando Suárez, Laura Cuy-Chaparro · 2020 · Revista Investigación en Salud Universidad de Boyacá
  9. Computational methods for functional analysis of plant small RNAs using the RNA degradome
    Joshua Thody · 2020 · UEA Digital Repository (University of East Anglia)
  10. Statistical methods for variant discovery and functional genomic analysis using next-generation sequencing data
    Man‐Lai Tang · 2020 · VTechWorks (Virginia Tech)
  11. A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples
    Gustavo Arango-Argoty, Lenwood S. Heath, Amy J. Pruden, Peter J. Vikesland, L. Zhang · 2021 · Lecture notes in computer science
  12. Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies.
    Yancy Lo · 2015 · Deep Blue (University of Michigan)
  13. Next-generation alignment tools
    Mohammad Yaseen Sofi, Afshana Shafi, Khalid Zaffar Masoodi · 2021 · Elsevier eBooks
  14. A study of RNA-editing in Populus trichocarpa nuclei revealed acquisition of RNA-editing on the endosymbiont-derived genes, and a preference for intracellular remodeling genes in adaptation to endosymbiosis
    Yiran Wang, Lihu Wang, Su Chen, Song Chen · 2021 · Forestry Research
  15. Bioinformatics of Human Genetic Disease Studies
    Dale J. Hedges · 2021 · Wiley eBooks
  16. Fuzzy k-mers and their application to comparative genome assembly
    Healy, John · 2013 · ARAN (University of Galway Research Repository) (Ollscoil na Gaillimhe – University of Galway)
  17. eDNA metabarcoding: a realistic perspective
    S. Moinier · 2013 · Utrecht University Repository (Utrecht University)
  18. References
    Ken Nguyen, Xuan Guo, Yi Feng Pan · 2016 · John Wiley & Sons, Inc. eBooks
  19. Bioinformatics Tools in Clinical Genomics
    David K. Crockett, Karl V. Voelkerding, Alan F. Brown, Rachel Lauren Stewart · 2018 · Springer eBooks
  20. Grand Celebration: 10th Anniversary of the Human Genome Project
    Rampelotto, Pabulo, John Burn, Lupski, James, Nelson, Karen · 2016 · MDPI eBooks
  21. The Bench Scientist’s Guide to Statistical Analysis of RNA-Seq Data
    Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram · 2014 · Apple Academic Press eBooks
  22. Analytical Approaches for Exome Sequence Data
    Andrew R Collins · 2018 · Translational bioinformatics
  23. Implementation of Genome Sequencing Assays
    Tina M. Hambuch, Keith Nykamp, Carri-Lyn Mead · 2018 · Springer eBooks
  24. Tag Sequencing
    Keerthana Krishnan, David Wood, Jason A. Steen, Sean Michael Grimmond, Nicole Cloonan · 2012 · Encyclopedia of Molecular Cell Biology and Molecular Medicine
  25. AVALIAÇÃO DA QUALIDADE DA MONTAGEM DE FRAGMENTOS DE SEQUÊNCIAS BIOLÓGICAS
    ALEJANDRO MUSTELIER MENES · 2017
  26. Computation for Genomics Knowledge Discovery
    Gregory Butler · 2015
  27. Peer Review #2 of "SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment (v0.1)"
    2017 · PeerJ
  28. DNA methods
    David Wesley Craig · 2012 · Cambridge University Press eBooks
  29. Peer Review #1 of "SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment (v0.2)"
    2017 · PeerJ
  30. Peer Review #2 of "SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment (v0.2)"
    2017 · PeerJ
  31. Bioinformatics Clouds for High-Throughput Technologies
    Claudia Cava, Francesca Gallivanone, Christian Salvatore, Pasquale Anthony Della Rosa, Isabella Castiglioni · 2014 · IGI Global eBooks
  32. Peer Review #1 of "SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment (v0.1)"
    2017 · PeerJ
  33. Current Massively Parallel Sequencing Technologies: Platforms and Reporting Considerations
    John R. ten Bosch, Wayne W. Grody · 2018 · Springer eBooks
  34. Unsupervised detection of interesting discrete sequences using Bayesian surprise
    Kenneth McGarry, Sharon McDonald, Dominic Button · 2022 · Research Square
  35. Cancer cells transfer invasive properties through tracks, a novel collagen-associated extracellular vesicle entity
    Léa Normand, Lucile Rouyer, Sylvaine Di-Tommaso, Cyril Dourthe, Anne‐Aurélie Raymond, Jean‐William Dupuy, Nathalie Allain, Nathalie Dugot‐Senant, Anthony Bouter, Alexandre Favereaux et al. · 2022 · Research Square
  36. Bioinformatic Methods for Identifying Differentially Abundant Subpopulations in scRNA-seq Data
    Giona Kleinberg, Ashwini Shinde, Sai Batchu, Michael Joseph Diaz, Kevin Thomas Root, Brandon Peter Lucke-Wold · 2022 · Preprints.org
  37. Molecular Detection and Identification of Candida
    Muataz Mohammed Al‐Taee · 2023 · IntechOpen eBooks
  38. Two-Cloud Private Read Alignment to a Public Reference Genome
    Sindhuja Madabushi, Parameswaran Ramanathan · 2023 · Proceedings on Privacy Enhancing Technologies
  39. Cancer cells transfer invasive properties through collagen-tracks
    Frédéric Saltel, Léa Normand, Lucile Rouyer, Élodie Richard, Nathalie Allain, Sylvaine Di-Tommaso, Cyril Dourthe, Anne‐Aurélie Raymond, Jean‐William Dupuy, Violaine Moreau et al. · 2023 · Research Square
  40. CareerMiner: Automatic extraction of professional network from large Chinese resume data
    Qiqi Chen, Dexu Kong, Yongchi Zhu, Zitao Shen, Chengyue Lu, Yang Li, Lin Zhang · 2023 · Franklin Open
  41. The De Bruijn Graph Sequence Mapping Problem with Changes in the Graph
    Lucas B. Rocha, Said Sadique Adi, Elói Araújo · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  42. seqtrie: Radix Tree and Trie-Based String Distances
    Travers H. Ching · 2023
  43. The application of omics tools in food mycology
    Ludwig Niessen, Josué José da Silva, Jens C. Frisvad, Marta Hiromi Taniwaki · 2024 · Advances in food and nutrition research
  44. Molecular Techniques
    Bijal A. Parikh, Andrew E. O. Hughes, Neil W. Anderson · 2023 · ClinMicroNow
  45. Bioinformatics in Primary Immunodeficiencies: Towards a “Computational Immunology” Era
    Josefina del Pilar Martínez Vásquez, Alexios‐Fotios A. Mentis · 2024 · Rare diseases of the immune system
  46. Molecular Techniques
    Bijal A. Parikh, Andrew E. O. Hughes, Neil W. Anderson · 2023 · ClinMicroNow
  47. Next Generation Sequence Analysis
    Payal Singh · 2025 · Elsevier eBooks
  48. Negative regulation of miRNAs sorting in EVs: the RNA-binding protein PCBP2 impairs SYNCRIP-mediated miRNAs EVs 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
  49. Negative regulation of miRNAs sorting in EVs: the RNA-binding protein PCBP2 impairs SYNCRIP-mediated miRNAs EVs 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
  50. Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression
    Jonah N. Cullen, Jakub Cieślak, Jessica L. Petersen, Rebecca R. Bellone, Carrie J. Finno, Ted Kalbfleisch, Kirstine Calløe, Stefano Capomaccio, Katia Cappelli, Stephen J. Coleman et al. · 2025 · PLoS Genetics
  51. Application of next-generation sequencing for detecting Mycoplasma contamination in veterinary vaccines
    Su-min Go, Yeonkyeong Lee, Jin-ju Nah, Hyun-Ok Gu, Il Jang, Min-Goo Seo · 2025 · Frontiers in Veterinary Science
  52. opjMap: A Sensitive Mapper for Repetitive Structural Variations in Long Noisy Reads Based on Orthogonal Projection
    Xing-Guo Fan, Xiaodan Zhang, Cheng-Song Hu, Jie-Jie Zeng, Shu-Rui Li, Ze‐Gang Wei · 2025 · Research Square
  53. Challenges of Next-Generation–Sequencing-Based Molecular Diagnostics
    C. Alexander Valencia, M. Ali Pervaiz, Ammar Husami, Yaping Qian, Kejian Zhang · 2013 · SpringerBriefs in genetics
  54. Supporting Quantitative Visual Analysis in Medicine and Biology in the Presence of Data Uncertainty
    Khoa Tan Nguyen · 2014 · Linköping University Electronic Press eBooks
  55. Additional file 1 of Technology dictates algorithms: recent developments in read alignment
    Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Taraszka, Kodi, Huwenbo Shi, Pelin Icer Baykal, Yang, Harry Taegyun, Victor Xue, Knyazev, Sergey, Singer, Benjamin D. et al. · 2021 · Figshare
  56. Additional file 1 of smsMap: mapping single molecule sequencing reads by locating the alignment starting positions
    Wei, Ze-Gang, Zhang, Shao-Wu, Liu, Fei · 2020 · Figshare
  57. Additional file 2 of Technology dictates algorithms: recent developments in read alignment
    Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Yang, Harry Taegyun, Victor Xue, Knyazev, Sergey, Singer, Benjamin D. et al. · 2021 · Figshare
  58. Additional file 1 of Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
    Köster, Johannes, Louis Dijkstra, Tobias Marschall, Alexander Schönhuth · 2020 · Figshare
  59. Additional file 3 of Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
    Köster, Johannes, Louis Dijkstra, Tobias Marschall, Alexander Schönhuth · 2020 · Figshare
  60. Additional file 1 of Improving somatic exome sequencing performance by biological replicates
    Yunus Emre Cebeci, Rumeysa Aslıhan Ertürk, Mehmet Arif Ergün, Mehmet Selman Baysan · 2024 · Figshare
  61. Disclosing and remodeling fungal macromolecules through in-silico analysis
    Quazi Mohd. Imranul Haq, Issa Sulaiman Al-Amri · 2025 · Elsevier eBooks
  62. Methods for Dynamic Optimization: Dynamic Programming and Pontryagin Method
    José M. Girón-Sierra · 2026 · Springer eBooks
  63. A general and extensible algorithmic framework to biological sequence alignment across scales and applications
    Hao Xuan, Hongyang Sun, Xiangtao Liu, Hanyuan Zhang, Jun Zhang, Cuncong Zhong · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. Noise-Resistant Event Sequence Embedding of IoT Malware
    Shun-Wen Hsiao, C. L. Philip Chen · 2025 · IEEE Annual Congress on Artificial Intelligence of Things (AIoT)
  65. Apports de l' analyse et l'intégration de données génomiques pour l'étude de la transcription et des réseaux de régulation dans le système hématopoïétique
    Cyrille Lepoivre · 2012
  66. Multi-dimensional and integrative pipeline for NGS-based datasets to explore cell fate decisions
    Mohamed-Ashick M. Saleem · 2015
  67. Etude des mécanismes de transmission de dérégulations épigénétiques : analyse de la transmission spermatique chez l'homme
    Céline Bruno · 2018 · theses.fr (ABES)
  68. Using the systematic nature of errors in NGS data to efficiently detect mutations : computational methods and application to early cancer detection
    Tiffany Myriam Delhomme · 2019 · theses.fr (ABES)
  69. Prédiction de la cinétique des inhibiteurs de protéines kinases et de leur affinité par docking flexible
    A. Braka · 2018
  70. From sequences to knowledge, improving and learning from sequence alignments
    Luc Blassel · 2022 · theses.fr (ABES)
  71. Functional Semantic Inference Method for Industrial Control Proprietary Protocol
    Yahui Yang, Yangyang Geng, Qiang Wei, Man Zhou, Zhuo Lv, Liupeng He · 2026 · IEEE Internet of Things Journal
  72. Central–local alignment and regional heterogeneity in China’s green building policy diffusion
    Yikun Su, Xinhao Gao, Zhizhe Zheng · 2026 · Environment Development and Sustainability
  73. Charting the Genetic Landscape and Clonal Architectures of Pheochromocytoma
    Joakim Crona · 2014 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
  74. Integration of Alignment and Phylogeny in the Whole-Genome Era
    Hongtao Sun · 2015
  75. Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Analysis Pipeline
    Erinija Pranckevičienė · 2015 · uO Research (University of Ottawa)
  76. Development of advanced computational systems for multiple sequence alignments by using heterogeneous biological information
    Francisco Manuel Ortuño · 2014 · Tesis Doctorals en Xarxa (Consorci de Serveis Universitaris de Catalunya)