Personalized copy number and segmental duplication maps using next-generation sequencing

Alkan, Can, Kidd, Jeffrey M, Marques-Bonet, Tomas, Aksay, Gozde, Antonacci, Francesca, Hormozdiari, Fereydoun, Kitzman, Jacob O, Baker, Carl +5 more·2009·Nature Genetics
DOI 10.1038/ng.437

Cited by (748)

Items 601–700 of 748

  1. Structural variation discovery: the easy, the hard and the ugly
    Fereydoun Hormozdiari · 2011 · Summit (Simon Fraser University)
  2. Genetic variation in the chicken genome: insights in selection
    Martin Elferink · 2011
  3. Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing data
    Yufeng Shen, Yiwei Gu, Itsik Pe’er · 2011 · IEEE International Conference on Computational Advances in Bio and Medical Sciences
  4. Fast and Accurate Mapping of Next Generation Sequencing Data
    Chandana Tikiri, Bandara Tennakoon · 2013
  5. Parallelization, scalability, and reproducibility in next generation sequencing analysis
    Johannes Köster · 2014 · Technische Universität Dortmund Eldorado (Technische Universität Dortmund)
  6. QuicK-mer: A rapid paralog sensitive CNV detection pipeline
    Feichen Shen, Jeffrey M. Kidd · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Detect Copy Number Variations from Read-depth of High-throughput Sequencing Data
    Wang, Weibo · 2019 · Carolina Digital Repository (University of North Carolina at Chapel Hill)
  8. Bioinformatics Analysis of Epigenetics
    Yanghua He, Jiuzhou Song · 2017 · Wiley eBooks
  9. DNA Sequence Alignment by Window based Optical Correlator
    Fereshte Mozafari, Hossein Babashah, Somayyeh Koohi, Zahra Kavehvash · 2017 · arXiv (Cornell University)
  10. Discovery of tandem and interspersed segmental duplications using high throughput sequencing
    Arda Söylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  11. CLEVER: Clique-Enumerating Variant Finder
    Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Johann Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth · 2012 · arXiv (Cornell University)
  12. CNVmap: a method and software to detect and map copy number variants from segregation data
    Matthieu Falque, Kamel Jebreen, Etienne Paux, Carsten Knaak, Sofiane Mezmouk, Olivier Martin · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  13. Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
    Damla Senol Cali · 2021 · arXiv (Cornell University)
  14. Comparative genomics on gene and single nucleotide level
    Jochen Blom · 2013 · Publikationen an der Universität Bielefeld (Universität Bielefeld)
  15. Recurrent CNVs in the Etiology of Epigenetic Neurodevelopmental Disorders
    Janine M. LaSalle, Mohammad Saharul Islam · 2013 · Springer eBooks
  16. Short history of the “Genomic Revolution” and implication for neurological institutes
    Stefano Gambardella, Veronica Albano, Rosa Campopiano, Rosangela Ferese, Simona Scala, Marianna Storto, Stefania Zampatti, Edoardo Romoli · 2014 · La Rivista Italiana della Medicina di Laboratorio - Italian Journal of Laboratory Medicine
  17. Efficient Statistical Models For Detecting And Analyzing Human Genetic Variations
    Zhanyong Wang · 2014 · eScholarship (California Digital Library)
  18. Genome-Wide Analyses of HIV-1 Host Genetics
    Kimberly Pelak · 2012 · DukeSpace (Duke University)
  19. Algorithms for structural variation discovery and protein-protein interaction prediction
    Iman Hajirasouliha · 2012 · Summit (Simon Fraser University)
  20. Experimental Design and Quality Control of Next‐Generation Sequencing Experiments
    Peter A.C. ’t Hoen, Matthew S. Hestand, Judith M. Boer, Yuching Lai, Maarten van Iterson, Michiel van Galen, Henk P.J. Buermans, Johan T. den Dunnen · 2011
  21. Genomes, Transcriptomes, Proteomes, and Bioinformatics
    Robert E. Farrell · 2010 · Elsevier eBooks
  22. CB-commander: a plugin based software suite for high throughput sequencing algorithms
    Reza Shahidi-Nejad · 2011 · Summit (Simon Fraser University)
  23. Multidimensional Context of Sequence Tags: Biological Data Integration
    Korbinian Grote, Thomas Werner · 2011
  24. Statistical Methods for the Analysis of Copy Number Variation
    Tan Hoang Nguyen · 2015 · Otago University Research Archive (University of Otago)
  25. Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs: A Dissertation
    Bo Han · 2015 · The Journal of the American Medical Association (JAMA) Network (American Medical Association)
  26. Deciphering regulation in eukaryotic cell: from sequence to function
    Valentina Boeva · 2014 · arXiv (Cornell University)
  27. Detection of rearrangement hotspots and their implication in complex human diseases
    Mohammed Jasaim Uddin · 2013 · Memorial University Research Repository (Memorial University)
  28. Characterising Structural Variation by Means of Next‐Generation Sequencing
    Chee‐Seng Ku, Nasheen Naidoo, Shu Mei Teo, Yudi Pawitan Y · 2011 · Encyclopedia of Life Sciences
  29. Assessment of copy number variations in the nebulin gene and other nemaline myopathy-causing genes
    K. Kiiski · 2015 · Työväentutkimus Vuosikirja
  30. LargeDEL: A tool for identifying large deletions in the whole genome sequencing data
    Pınar Kavak, Hüseyin Demirci · 2015 · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
  31. Molecular karyotyping in routine diagnostics – a view back and forth1)
    Uwe Heinrich, Meike Gabert, Imma Rost · 2013 · Journal of Laboratory Medicine
  32. Correction: Nucleotide, Cytogenetic and Expression Impact of the Human Chromosome 8p23.1 Inversion Polymorphism
    Nina Bosch, Marta Morell, Immaculada Ponsa, Josep Maria Mercader, Lluı́s Armengol, Xavier Estivill · 2010 · PLoS ONE
  33. The algorithm of equal acceptance region for detecting copy number alterations: applications to next-generation sequencing data
    Yan‐Xia Lin · 2012 · International Journal of Bioinformatics Research and Applications
  34. HeurAA: Accurate and Fast Detection of Genetic Variations with a Novel Heuristic Amplicon Aligner Program for Next Generation Sequencing
    Lőrinc Sándor Pongor, Ferenc Pintér, István Peták · 2013 · PLoS ONE
  35. Detection of novel tandem duplication with next-generation sequencing
    Xuan Liu, Shing Wan Choi, Thomas K. F. Wong, Tak‐Wah Lam, Siu‐Ming Yiu · 2011 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  36. Computational Biology-Driven Genomic and Epigenomic Delineation of Acute Myeloid Leukemia
    Mathijs Arnoud Sanders · 2015 · EUR Research Repository (Erasmus University Rotterdam)
  37. Memory efficient assembly of human genome
    Farhad Hormozdiari, Eleazar Eskin · 2014 · Journal of Bioinformatics and Computational Biology
  38. Engineering Algorithms for Personal Genome Pipelines
    Manuel Holtgrewe · 2015 · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver
  39. Neurodevelopmental Genomics of Autism, Schizophrenia, and Related Disorders
    J.F. Cubells, Daniel Moreno‐De‐Luca · 2013 · Elsevier eBooks
  40. Analytical Approaches for Exome Sequence Data
    Andrew R Collins · 2012 · Translational bioinformatics
  41. APPLICATIONS OF NEXT-GENERATI ON SEQUENCING REVIEWS
    Can Alkan, Evan E. Eichler · 2011
  42. METHOD Open Access
    Lasse Maretty, Jonas A. Sibbesen, Anders Krogh · 2014
  43. แนวทางใหมมาณดเอนเอเปาหมายอยางสมบโดยใชปฏรกโซ พอลด Droplet Digital Polymerase Chain Reaction: A Novel Method for Absolute Quantifi cation of the Target DNA
    Nattharat Jearapong, Kanokwan Jarukamjorn · 2013
  44. This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. Towards a comprehensive structural variation map of an individual human genome
    Jeffrey R. MacDonald, Muhammad Rafiq, Donald F. Conrad, Charles Lee, Lars Feuk, Stephen W. Scherer · 2010
  45. DEVELOPING NEW TOOLS FOR DETECTING GERMLINE
    Marc A. Beal · 2012
  46. Using exome sequencing to study adaptive evolution in non-human primates and human populations
    Renee D. George · 2012 · ResearchWorks at the University of Washington (University of Washington)
  47. Understanding the impact of chromosomal inversion on the evolution of the human genome
    João M. Alves · 2014 · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
  48. Reduced representations for efficient analysis of genomic data
    Md Pavel Mahmud · 2014
  49. Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism
    Ryan Delahanty · 2010
  50. other nemaline myopathy- - causing genes genes
    K. Kiiski · 2015
  51. Organizational Heterogeneity of the Human Genome: Significant Variation of Recombination Rate of 100 kbp Sequences within GC Ranges
    Svetlana Frenkel, Valery M. Kirzhner, Zeev Frenkel, Abraham Korol · 2016 · International Symposium on Stochastic Models in Reliability Engineering, Life Science and Operations Management
  52. Besonderheiten der Genomsequenzierung als Grundlage der Steuerung in der translationalen Medizin
    Fruzsina Molnár‐Gábor · 2015 · Springer eBooks
  53. The Human Genome
    Daryl A. Scott, Brendan Lee · 2011 · Elsevier eBooks
  54. Computational Approaches for Finding Long Insertions and Deletions with NGS Data
    Jin Zhang, Chong Chu, Yufeng Wu · 2016
  55. Hybridization and amplification rate correction for
    Quan Wang, Peichao Peng, Minping Qian, Lin Wan, Minghua Deng · 2012
  56. Análisis, validación y estudio poblacional de las inversiones entre dos genomas humanos
    David Salvador · 2014 · TDX (Tesis Doctorals en Xarxa)
  57. The evolution of the paleopolyploid genome in family Salicaceae
    Eli Rodgers‐Melnick · 2013
  58. Gene expression and copy number variation in common complex diseases
    Britney L. Grayson · 2010
  59. Desenvolvimento de um teste para a trissomia do cromossomo 21 através da análise de ácidos nucleicos fetais no plasma materno por sequenciamento de última geração
    Renata Moscolini Romão · 2016
  60. Leveraging Similar Regions to Improve Genome Data Processing
    Kristal Curtis · 2015 · eScholarship (California Digital Library)
  61. Identifying Susceptibility Genes for Familial Pancreatic Cancer Using Novel High-Resolution Genome Interrogation Platforms
    Wigdan Al-Sukhni · 2012 · TSpace (University of Toronto)
  62. Systematic Analysis of Duplications and Deletions in the Malaria Parasite P. falciparum: A Dissertation
    Derrick K. DeConti · 2015 · The Journal of the American Medical Association (JAMA) Network (American Medical Association)
  63. Short history of the "Genomic Revolution" and implication for neurological institutes Breve storia della "Rivoluzione Genomica" e sue implicazioni per gli istituti neurologici
    Stefano Gambardella, V. Albano, Rosa Campopiano, Rosangela Ferese, Simona Scala, Marianna Storto, Stefania Zampatti, Edoardo Romoli · 2015
  64. Methods for the Detection of Single Nucleotide Variants and Indels from Cell-Free DNA
    Can Koçkan · 2016 · Summit (Simon Fraser University)
  65. Computational Approaches for Variant Identification
    Diksha Garg, Ankita Jiwan, Shailendra Singh · 2017 · International Journal of Computer Applications
  66. Identification and analysis of recently duplicated genes in channel catfish (Ictalurus punctatus) genome
    Yu Zhang · 2013
  67. EPiC Series in Computing
    Goran Frehse, Matthias Althoff · 2017 · Institute of Science and Technology Austria
  68. Genomes, Transcriptomes, Proteomes, and Bioinformatics
    Robert E. Farrell · 2017 · Elsevier eBooks
  69. STATISTICAL METHODS FOR ASSESSING STRUCTURAL CHANGE IN HUMAN & MICROBIAL GENOMES
    Xuan Zhu · 2017 · Digital Commons-TMC (Texas Medical Center)
  70. Fast and Sensitive Genome-Hashing Software and its Application in Using NGS as a Detection Agent for Bacterial Presence in Oral Metagenomic Samples - August, 2015
    Paul M. Gontarz · 2015 · IRL - University of Missouri, St. Louis (University of Missouri–St. Louis)
  71. Computational methods for analyzing ngs data to discover clinically relevant mutations
    Bekir Ergüner · 2017 · Sabanci University
  72. Algorithms for structural variation discovery using multiple sequence signatures
    Arda Söylev · 2018 · Bilkent University Institutional Repository (Bilkent University)
  73. Algorithms for Analyzing Human Genome Rearrangements
    Crystal L. Kahn · 2011
  74. Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design
    Mohammed Alser · 2019 · arXiv (Cornell University)
  75. Variant Calling in Next Generation Sequencing Data
    Jennifer D. Hintzsche, William Allen Robinson, Aik Choon Tan · 2019 · Elsevier eBooks
  76. Long-term balancing selection in the genomes of humans and other great apes
    João C. Teixeira · 2016 · Qucosa (Saxon State and University Library Dresden)
  77. Detection of somatic variants from genomic data and their role in neurodegenerative diseases
    Irene Lobón García · 2019 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
  78. Alterações de número de cópias genômicas em hepatoblastomas: microarranjos genômicos e sequenciamento de nova geração
    Juliana Sobral de Barros · 2020
  79. Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning
    Furkan Özden, Can Alkan, A. Ercüment Çiçek · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  80. Accelerated Filtering and in situ Verification for Energy-Optimized Genome Read Mapping
    Venkateshwarlu Yellaswamy Gudur, Sidharth Maheshwari, Rishad Shafik, Amit Acharyya · 2020 · IEEE International Symposium on Circuits and Systems proceedings
  81. 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
  82. Large structural variation discovery using long reads with several degrees of error
    Ezgi Ebren · 2020 · Bilkent University Institutional Repository (Bilkent University)
  83. Statistical Applications in Genetics and Molecular Biology
    Michael I. Love, Ruping Sun, Vera M. Kalscheuer · 2011
  84. Read-depth Methodology for the Analysis of Recent Segmental Duplications in the Grapevine Genome
    Giuliana Giannuzzi, Maria Francesca Cardone, Marco Ventura, Donato Antonacci · 2013
  85. Bioinformatics of Human Genetic Disease Studies
    Dale J. Hedges · 2021 · Wiley eBooks
  86. Efficient algorithms for human genetic variation detection using high-throughput sequencing techniques
    Eleazar Eskin, Dan He · 2012
  87. Detecção de variações genômicas em bovinos da raça nelore usando dados de genotipagem e ressequenciamento
    Joaquim Manoel da Silva · 2015
  88. Analytical Approaches for Exome Sequence Data
    Andrew R Collins · 2018 · Translational bioinformatics
  89. Peer Review #1 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.2)"
    2014 · PeerJ
  90. Analysis Pipelines for Next- Generation Sequencing Data
    Jung Soh, Paul M.K. Gordon, Christoph W. Sensen · 2012 · Chapman & Hall/CRC mathematical and computational biology series
  91. Peer Review #1 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.1)"
    2014 · PeerJ
  92. Correction: PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data
    Geà rgia Escaramís, Cristian Tornador, Laia Bassaganyas, Raquel Rabionet, José M. C. Tubío, Alexander Martinez‐Fundichely, Mario Cáceres, Marta Gut, Stephan Ossowski, Xavier Estivill · 2013 · PLoS ONE
  93. Faculty Opinions recommendation of Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae).
    Norman Johnson · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  94. Peer Review #3 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.1)"
    2014 · PeerJ
  95. Peer Review #3 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.2)"
    2014 · PeerJ
  96. Peer Review #2 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.1)"
    2014 · PeerJ
  97. Peer Review #2 of "Massively parallel read mapping on GPUs with the q-group index and PEANUT (v0.2)"
    2014 · PeerJ
  98. The Mechanisms and Consequences of DNA Re-replication
    Jie Lin · 2011
  99. Faculty Opinions recommendation of CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data.
    Deborah Charlesworth · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  100. Faculty Opinions recommendation of Accelerated growth in the absence of DNA replication origins.
    Ueli Schibler · 2013 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature