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 401–500 of 748

  1. On the core segmentation algorithms of copy number variation detection tools
    Yibo Zhang, Wenyu Liu, Junbo Duan · 2024 · Briefings in Bioinformatics
  2. Detection and Interpretation of Genomic Structural Variation in Mammals
    Ira M. Hall, Aaron R. Quinlan · 2011 · Methods in molecular biology
  3. 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
  4. COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples
    Neeraja M. Krishnan, Prakhar Gaur, Rakshit Chaudhary, Arjun Arkal Rao, Binay Panda · 2012 · PLoS ONE
  5. Detection and interpretation of genomic structural variation in health and disease
    Geert Vandeweyer, R. Frank Kooy · 2012 · Expert Review of Molecular Diagnostics
  6. USP17-mediated de-ubiquitination and cancer: Clients cluster around the cell cycle
    Charles E. Ducker, Peter E. Shaw · 2020 · The International Journal of Biochemistry & Cell Biology
  7. MoGUL: Detecting Common Insertions and Deletions in a Population
    Seunghak Lee, Eric P. Xing, Michael Brudno · 2010 · Lecture notes in computer science
  8. Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads
    Alexander J. Nederbragt, Trine B. Rounge, Kyrre Kausrud, Kjetill S. Jakobsen · 2010 · Sequencing
  9. High-resolution fish on DNA fibers for low-copy repeats genome architecture studies
    Òscar Molina, Joan Blanco, Ester Antón, Francesca Vidal, Emanuela Valeria Volpi · 2012 · Genomics
  10. Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes
    Diogo Pratas, Raquel Monteiro Silva, Armando J. Pinho · 2018 · Entropy
  11. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes
    Ahmed Ibrahim Samir Khalil, Costerwell Khyriem, Anupam Chattopadhyay, Amartya Sanyal · 2020 · BMC Bioinformatics
  12. Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses
    Mrinmoy Ghosh, Hyun-Woo Cho, Jeong-Woong Park, Jaeyoung Choi, Young-Hwa Chung, Neelesh Sharma, Amit Kumar Singh, Nam Eun Kim, Raj Kumar Mongre, Do Luong Huynh et al. · 2016 · Applied Biochemistry and Biotechnology
  13. A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation
    Sandra Louzada, Ana Vieira-da-Silva, Ana Mendes-da-Silva, Svatava Kubı́čková, Jiřı́ Rubeš, Filomena Adega, Raquel Chaves · 2015 · Molecular Phylogenetics and Evolution
  14. How genome complexity can explain the difficulty of aligning reads to genomes
    Vinhthuy Phan, Shanshan Gao, Quang Tran, Nam S. Vo · 2015 · BMC Bioinformatics
  15. Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers
    Shay Zakov, Vineet Bafna · 2015 · Journal of Computational Biology
  16. The Challenges of Studying Complex and Dynamic Regions of the Human Genome
    Edward J. Hollox · 2011 · Methods in molecular biology
  17. S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light
    Xiaohui Duan, Kai Xu, Yuandong Chan, Christian Hundt, Bertil Schmidt, Pavan Balaji, Weiguo Liu · 2017 · IEEE International Conference on Cluster Computing (CLUSTER)
  18. Accelerating FM-index Search for Genomic Data Processing
    Yuanrong Wang, Xueqi Li, Dawei Zang, Guangming Tan, Ninghui Sun · 2018 · Proceedings of the International Conference on Parallel Processing
  19. Polishing copy number variant calls on exome sequencing data via deep learning
    Furkan Özden, Can Alkan, A. Ercüment Çiçek · 2022 · Genome Research
  20. Structural variation, selection, and diversification of the NPIP gene family from the human pangenome
    Philip C. Dishuck, Katherine M. Munson, Alexandra P. Lewis, Max L. Dougherty, Jason G. Underwood, William T. Harvey, PingHsun Hsieh, Tomi Pastinen, Evan E. Eichler · 2025 · Cell Genomics
  21. GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
    Zülal Bingöl, Mohammed Alser, Onur Mutlu, Özcan Öztürk, Can Alkan · 2021 · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum
  22. What Have Studies of Genomic Disorders Taught Us About Our Genome?
    Alexandra D. Simmons, Claudia M.B. Carvalho, James R. Lupski · 2011 · Methods in molecular biology
  23. Developing a New qPCR‐Based System for Screening Mutation
    Junjie Zhu, Yanfeng Zhao, Ming Liu, Diego González-Rivas, Xinnan Xu, Weijing Cai, Huiwei Qi, Lei Dai, Zijian Wang, Xiao Song et al. · 2019 · Small
  24. Copy number variations among silkworms
    Qian Zhao, Minjin Han, Wei Sun, Ze Zhang · 2014 · BMC Genomics
  25. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis )
    Shuli Liu, Xiaolong Kang, Claudia Rita Catacchio, Mei Liu, Lingzhao Fang, Steven Schroeder, Wenli Li, Benjamin D. Rosen, Daniela Iamartino, L. Iannuzzi et al. · 2019 · Functional & Integrative Genomics
  26. Sequence Alignment Tools: One Parallel Pattern to Rule Them All?
    Claudia Misale, Giulio Ferrero, Massimo Torquati, Marco Aldinucci · 2014 · BioMed Research International
  27. Efficient In Silico Identification of a Common Insertion in the MAK Gene which Causes Retinitis Pigmentosa
    Kinga M. Bujakowska, Joseph White, Emily Place, Mark B. Consugar, Jason Comander · 2015 · PLoS ONE
  28. Single-Cell Copy Number Analysis of Prostate Cancer Cells Captured with Geometrically Enhanced Differential Immunocapture Microdevices
    Erica D. Pratt, Asya Stepansky, James B Hicks, Brian J. Kirby · 2014 · Analytical Chemistry
  29. Towards Selective-Alignment
    Hirak Sarkar, Mohsen Zakeri, Laraib Iqbal Malik, Rob Patro · 2018 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  30. CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B
    Hoang T. Nguyen, Tony Raymond Merriman, Michael A. Black · 2013 · PLoS ONE
  31. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches
    Meznah Almutairy, Eric K. Torng · 2018 · PLoS ONE
  32. BagGMM: Calling copy number variation by bagging multiple Gaussian mixture models from tumor and matched normal next-generation sequencing data
    Yaoyao Li, Junying Zhang, Xiguo Yuan · 2019 · Digital Signal Processing
  33. A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes
    Fahad Saeed, Alan Perez-Rathke, Jaroslaw Gwarnicki, Tanya Y. Berger-Wolf, Ashfaq Khokhar · 2011 · Journal of Parallel and Distributed Computing
  34. Autozygome maps dispensable DNA and reveals potential selective bias against nullizygosity
    Hanif G. Khalak, Salma Majid Wakil, Faiqa Imtiaz, Khushnooda Ramzan, Batoul Baz, Abeer Al‐Mostafa, Samya T. Hagos, Fatema Alzahrani, Nada Abu Dhaim, Leen Abu‐Safieh et al. · 2012 · Genetics in Medicine
  35. Accurate and sensitive single-cell-level detection of copy number variations by micro-channel multiple displacement amplification (μcMDA)
    Junji Li, Na Lü, Yuhan Tao, Mengqin Duan, Yi Qiao, Yuming Xu, Qinyu Ge, Changwei Bi, Jiye Fu, Jing Tu et al. · 2018 · Nanoscale
  36. Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast
    Nathaniel P. Sharp, Denise R. Smith, Gregory Driscoll, Kexin Sun, Catherine M. Vickerman, Sterling C.T. Martin · 2023 · Genome Biology and Evolution
  37. A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data
    Shuoguo Wang, Jinchuan Xing · 2013 · Genomics & Informatics
  38. An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women
    Sunshin Kim, HeeJung Jung, Sung Hee Han, Seung Jae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Kyudong Han, Hwanjong Kwak, Sung‐Hoon Park et al. · 2016 · BMC Medical Genomics
  39. Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children
    Diana Lizzete Antúnez-Ortiz, Eugenia Flores‐Alfaro, Ana I. Burguete-García, Amélie Bonnefond, Jesús Peralta‐Romero, Philippe Froguel, Mónica Espinoza-Rojo, Miguel Cruz · 2017 · BioMed Research International
  40. New clinical molecular diagnostic methods for congenital and inherited heart disease
    Jan D.H. Jongbloed, Anna Pósafalvi, Wilhelmina S. Kerstjens‐Frederikse, Richard J. Sinke, J. Peter van Tintelen · 2010 · Expert Opinion on Medical Diagnostics
  41. Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons
    Wahab A. Khan, Joan H.M. Knoll, Peter K. Rogan · 2011 · Molecular Cytogenetics
  42. Genome reassembly with high-throughput sequencing data
    Nathaniel Parrish, Benny Sudakov C, Eleazar Eskin · 2013 · BMC Genomics
  43. Exploring structural variants in environmentally sensitive gene families
    Nevin Dale Young, Peng Zhou, Kevin A.T. Silverstein · 2016 · Current Opinion in Plant Biology
  44. Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans
    Cemalettin Bekpen, Sven Künzel, Chen Xie, Muthukrishnan Eaaswarkhanth, Yen‐Lung Lin, Ömer Gökçümen, Cezmi A. Akdiş, Diethard Tautz · 2017 · BMC Genomics
  45. PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping
    Ming-Hsin Tsai, Yen‐Yi Liu, Von‐Wun Soo · 2017 · Frontiers in Microbiology
  46. Calling amplified haplotypes in next generation tumor sequence data
    Ninad Dewal, Yang Hu, Matthew L. Freedman, Thomas LaFramboise, Itsik Pe’er · 2011 · Genome Research
  47. Rapid adaptive increase of amylase gene copy number in Indigenous Andeans
    Kendra Scheer, Luane J. B. Landau, Kelsey C. Jorgensen, Charikleia Karageorgiou, Lindsey Siao, Can Alkan, Angelis M. Morales Rivera, Christopher A. Osborne, Obed A. Garcia, Laurel Pearson et al. · 2026 · Nature Communications
  48. Intrinsic Disorder in Human Proteins Encoded by Core Duplicon Gene Families
    Nathan W Van Bibber, Cornelia Haerle, Roy Khalife, Guy W. Dayhoff, Vladimir Nikolaevich Uversky · 2020 · The Journal of Physical Chemistry B
  49. ASMCap: An Approximate String Matching Accelerator for Genome Sequence Analysis Based on Capacitive Content Addressable Memory
    Hongtao Zhong, Zhonghao Chen, Wenqin Huangfu, Chen Wang, Yixin Xu, Tianyi Wang, Yao Yu, Yongpan Liu, Vijaykrishnan Narayanan, Huazhong Yang et al. · 2023 · ACM/IEEE Design Automation Conference (DAC)
  50. A Multi-Sample Based Method for Identifying Common CNVs in Normal Human Genomic Structure Using High-Resolution aCGH Data
    Chihyun Park, Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park · 2011 · PLoS ONE
  51. Copy number variation signature to predict human ancestry
    Melissa Pronold, Marzieh Vali, Roger Piqué-Regi, Shahab Asgharzadeh · 2012 · BMC Bioinformatics
  52. TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
    Danai Fimereli, Vincent Detours, Tomasz Konopka · 2013 · Nucleic Acids Research
  53. Involvement of SPATA31 copy number variable genes in human lifespan
    Cemalettin Bekpen, Chen Xie, Almut Nebel, Diethard Tautz · 2018 · Aging
  54. Speeding up DNA sequence alignment by optical correlator
    Fereshte Mozafari, Hossein Babashah, Somayyeh Koohi, Zahra Kavehvash · 2018 · Optics & Laser Technology
  55. SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees
    Aleksandr O. Morgulis, Richa Agarwala · 2020 · GigaScience
  56. Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing
    Minxuan Zhou, Lingxi Wu, Muzhou Li, Niema Moshiri, Kevin Skadron Y, Tajana Rosing · 2021 · International Conference on Parallel Architectures and Compilation Techniques (PACT)
  57. Fast and accurate mapping of Complete Genomics reads
    Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Onur Mutlu, Can Alkan · 2014 · Methods
  58. Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates
    Flavia Angela Maria Maggiolini, Ludovica Mercuri, Francesca Antonacci, Fabio Anaclerio, Francesco Maria Calabrese, Nicola Lorusso, Alberto L’Abbate, Melanie Sorensen, Giuliana Giannuzzi, Evan E. Eichler et al. · 2020 · Genes
  59. Assembly of Non-Unique Insertion Content Using Next-Generation Sequencing
    Nathaniel Parrish, Farhad Hormozdiari, Eleazar Eskin · 2014 · Apple Academic Press eBooks
  60. Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes
    Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Şahinalp · 2011 · Lecture notes in computer science
  61. Between a chicken and a grape: estimating the number of human genes
    Mihaela Pertea, Steven L. Salzberg · 2010 · Genome biology
  62. MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
    Melina Soysal, Konstantina Koliogeorgi, Can Fırtına, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco de Oliveira Junior, Yu Liang, Klea Zambaku, Mohammad Sadrosadati et al. · 2025 · International Conference on Supercomputing
  63. Reprever: resolving low-copy duplicated sequences using template driven assembly
    Sangwoo Kim, Paul Medvedev, Tara Paton, Vineet Bafna · 2013 · Nucleic Acids Research
  64. GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
    Zülal Bingöl, Mohammed Alser, Onur Mutlu, Özcan Öztürk, Can Alkan · 2024 · IEEE Transactions on Computers
  65. Accelerating Bowtie2 with a lock-less concurrency approach and memory affinity
    Claudia Misale · 2014 · Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)
  66. Nucleotide Sequence Alignment and Compression via Shortest Unique Substring
    Boran Adaş, Ersin Bayraktar, Simone Faro, Ibraheem Elsayed Moustafa, Muhammed Oğuzhan Külekci · 2015 · Lecture notes in computer science
  67. Detection of chromosome abnormalities using current noninvasive prenatal testing: A multi-center comparative study
    Yan Du, Jing Lin, Likun Lan, Ying Xu Dong, Jun Zhu, Wen Jiang, Xinyao Pan, Youhui Lu, Da‐Jin Li, Ling Wang · 2018 · BioScience Trends
  68. Mendelian randomization: potential use of genetics to enable causal inferences regarding HIV-associated biomarkers and outcomes
    Weijing He, John Castiblanco, Elizabeth A Walter, Jason F. Okulicz, Sunil K. Ahuja · 2010 · Current Opinion in HIV and AIDS
  69. Detection Copy Number Variants from NGS with Sparse and Smooth Constraints
    Yue Zhang, Yiu‐ming Cheung, Bo Xu, Weifeng Su · 2016 · IEEE Transactions on Computational Biology and Bioinformatics
  70. Development and Validation of a 34‐Gene Inherited Cancer Predisposition Panel Using Next‐Generation Sequencing
    Sun Hee Rosenthal, Weimin Sun, Ke Zhang, Yan Liu, Quoclinh Nguyen, Anna V Gerasimova, Camille R. Nery, Linda L. Cheng, Carolyn Castonguay, Elaine H. Hiller et al. · 2020 · BioMed Research International
  71. ALPHA: A Novel Algorithm-Hardware Co-Design for Accelerating DNA Seed Location Filtering
    Fazal Hameed, Asif Ali Khan, Jerónimo Castrillón · 2021 · IEEE Transactions on Emerging Topics in Computing
  72. GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level
    Benjamin Spiegl, Faruk Kapidzic, Sebastian Röner, Martin Kircher, Michael R. Speicher · 2023 · NAR Genomics and Bioinformatics
  73. Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries
    Xander Nuttle, Nicholas D. Burt, Benjamin Currall, Mariana Moysés‐Oliveira, Kiana Mohajeri, Riya Bhavsar, Diane E. Lucente, Rachita Yadav, Derek J.C. Tai, James F. Gusella et al. · 2023 · Cell Reports Methods
  74. AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read Mapping
    Ngoc Hieu Tran, Xin Chen · 2015 · IEEE Transactions on Computational Biology and Bioinformatics
  75. Approximate jitter probability in the breakpoints of genome copy number variations
    Jorge Muñoz‐Minjares, Yuriy S. Shmaliy · 2013 · International Conference on Electrical Engineering, Computing Science and Automatic Control (CCE)
  76. Benchmarking Short Sequence Mapping Tools
    Ayat Hatem, Doruk Bozdağ, Ümit V. Çatalyürek · 2011 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  77. Parsimony and likelihood reconstruction of human segmental duplications
    Crystal L. Kahn, Borislav Hrisimirov Hristov, Benjamin J. Raphael · 2010 · Bioinformatics
  78. DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment
    Changyong Yu, Yuhai Zhao, Chu Zhao, Haitao Ma, Guoren Wang · 2021 · IEEE Transactions on Computational Biology and Bioinformatics
  79. A method for improving the accuracy of non-invasive prenatal screening by cell-free foetal DNA size selection
    QZ He, XJ Wu, QY He, Jin-Lian Xiang, Chaohua Zhang, Li‐Che Lu, T Wang, H Li · 2018 · British Journal of Biomedical Science
  80. Cloudbreak: Accurate and Scalable Genomic Structural Variation Detection in the Cloud with MapReduce
    Christopher W. Whelan, Jeffrey W Tyner, Alberto L’Abbate, Clelia Tiziana Storlazzi, Lucia Carbone, Kemal Sönmez · 2013 · arXiv (Cornell University)
  81. Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work
    Atalay Mert İleri, Halil Ibrahim Ozercan, Alper Gündogdu, Ahmet K. Senol, M. Yusuf Özkaya, Can Alkan · 2016 · arXiv (Cornell University)
  82. A Workload and Programming Ease Driven Perspective of Processing-in-Memory
    Saugata Ghose, Amirali Boroumand, Jeremie S. Kim, Juan Gómez-Luna, Onur Mutlu · 2019 · arXiv (Cornell University)
  83. A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes
    Saimire Silaiyiman, Jiaxuan Liu, Jiaxin Wu, Lejun Ouyang, Zheng Cao, Chao Shen · 2025 · Plants
  84. Noninvasive Prenatal Screening for Common Fetal Aneuploidies Using Single-Molecule Sequencing
    Yeqing Qian, Yongfeng Liu, Kai Yan, Yanfei Xu, Yixi Sun, Gao Xiaoyang, Na Chen, Pengzhen Jin, Lidong Zeng, Lei Sun et al. · 2023 · Laboratory Investigation
  85. GEM: Ultra-Efficient Near-Memory Reconfigurable Acceleration for Read Mapping by Dividing and Predictive Scattering
    Longlong Chen, Jianfeng Zhu, Guiqiang Peng, Mingxu Liu, Shaojun Wei, Leibo Liu · 2023 · IEEE Transactions on Parallel and Distributed Systems
  86. QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms
    Julián Pavón, Ivan Vargas Valdivieso, Carlos Rojas, César Hernández, Mehmet Aslan, Roger Figueras, Yichao Yuan, Joël Lindegger, Mohammed Alser, Francesc Moll et al. · 2024 · Proceedings - International Symposium on Computer Architecture/Proceedings
  87. Genome-wide patterns of genetic variation among silkworms
    Xingtan Zhang, Mengyun Nie, Qian Zhao, Yuqian Wu, Genhong Wang, Qingyou Xia · 2015 · Molecular Genetics and Genomics
  88. Massively parallel read mapping on GPUs with the q -group index and PEANUT
    Johannes Köster, Sven Rahmann · 2014 · PeerJ
  89. RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data
    Yuting He, Fan Zhang, Patrick Flaherty · 2015 · Bioinformatics
  90. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data
    Arda Söylev, Sevim Seda Çokoğlu, Dilek Koptekin, Can Alkan, Mehmet Somel · 2022 · PLoS Computational Biology
  91. Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline
    Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha A. Datta, Charles D. Johnson · 2015 · IEEE Transactions on Computational Biology and Bioinformatics
  92. Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects
    Francisco Ferreira Do Nascimento, Katia S. Guimarães · 2016 · IEEE Transactions on Computational Biology and Bioinformatics
  93. Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis
    Daria V. Zhernakova, Sergei F. Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel V. Dobrynin, Andrey A. Yurchenko et al. · 2018 · PLoS ONE
  94. Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine
    Yaqiong Jin, Geng Chen, Wenming Xiao, Huixiao Hong, Joshua Xu, Yongli Guo, Wenzhong Xiao, Tieliu Shi, Leming M. Shi, Weida Tong et al. · 2019 · Science China Life Sciences
  95. Ψ-RA: a parallel sparse index for genomic read alignment
    Muhammed Oğuzhan Külekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter, Bojian Xu · 2011 · BMC Genomics
  96. Indices and Applications in High-Throughput Sequencing
    David Weese · 2013 · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver
  97. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-Seq data
    Mingxiang Teng, Rafael A. Irizarry · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  98. DAGIP: alleviating cell-free DNA sequencing biases with optimal transport
    Antoine Passemiers, Stefania Tuveri, Tatjana Jatsenko, Adriaan Vanderstichele, Pieter Busschaert, An Coosemans, Dirk Timmerman, Sabine Tejpar, Peter Vandenberghe, Diether Lambrechts et al. · 2025 · Genome biology
  99. Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees
    Md Pavel Mahmud, John Wiedenhoeft, Alexander Schliep · 2012 · Bioinformatics
  100. Crescent: A GPU-based Targeted Nanopore Sequence Selector
    Tong Li, Xueqi Li, Yewen Li, Ruibao Song, Xun Wang · 2022 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)