Genome-wide profiling of heritable and de novo STR variations

Willems, Thomas, Zielinski, Dina, Yuan, Jie, Gordon, Assaf, Gymrek, Melissa, Erlich, Yaniv·2017·Nature Methods
DOI 10.1038/nmeth.4267

Cited by (355)

Items 201–300 of 355

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  3. Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms
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  9. STRAS:a snakemake pipeline for genome-wide short tandem repeats annotation and score
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  12. Fitness landscapes of human microsatellites
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  13. Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution
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  14. Global prevalence of potentially pathogenic short-tandem repeats in an epilepsy cohort
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  16. Phenotypic associations with the HMOX1 GT(n) promoter repeat in European populations
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  18. Exome-wide tandem repeats confer large effects on subcortical volumes in UK Biobank participants
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  21. Systematic evaluation of the impact of promoter proximal short tandem repeats on expression
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  23. Genome-wide discovery of polymorphic simple sequence repeat (SSR) markers through comparative analysis of closely related hami melon cultivars
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  26. Genome-wide discovery of short sequence repeat markers useful for genetic diversity studies in Lima bean (Phaseolus lunatus L.)
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  28. HipSTR-UI: A cross-platform graphical interface for accessible str genotyping from next-generation sequencing data
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  29. The Development of New SSR Markers and an Assay for Genotyping Sweet Cherry (Prunus avium L.) in One Reaction
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  30. Genomics of Sable (Martes zibellina) × Pine Marten (Martes martes) Hybridization
    Andrey A. Tomarovsky, Azamat A. Totikov, Tatiana M. Bulyonkova, P. Perelman, Alexei V. Abramov, N. A. Serdyukova, Aliya R. Yakupova, D. Prokopov, V. Beklemisheva, Mikkel-Holger S. Sinding et al. · 2025 · bioRxiv
  31. The selective dynamics of interruptions at short tandem repeats
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  32. Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects
    Yevgeniy Plavskin, Maria Stella de Biase, Naomi Ziv, Libuše Janská, Yuan O. Zhu, David W. Hall, Roland F. Schwarz, Daniel Tranchina, Mark L. Siegal · 2024 · PLoS Biology
  33. Assessing sequence variation and genetic diversity of currently untapped Y-STR loci
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  34. Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola
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  35. BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes
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  36. Multi-ancestry tandem repeat association study of hair colour using exome-wide sequencing
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  37. Large-scale genotyping and meta-analysis of PIEZO1 short tandem repeat alleles suggest a modest association with malaria susceptibility
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  38. Identification of (ultra-)rare functional promoter mutations in cancer using sequence-based deep learning models
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  39. Estimating the size of long tandem repeat expansions from short reads with ScatTR
    Rashid Al-Abri, Gamze Gürsoy · 2025 · Genome Research
  40. Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions
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  41. Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution
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  42. Absence of pathogenic Short Tandem Repeat expansions in Systemic Lupus Erythematosus disease-associated genes
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  43. bMSI-CAST: a systematic method for next generation sequencing-based microsatellite instability detection in plasma cell-free DNA
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  44. Open-Access STRS Database Of Populations From The 1000 Genomes Project Using High Coverage Phase 3 Data
    Tamara Soledad Frontanilla Recalde, Guilherme Silva, Jesús Ayala, Celso Teixeira Mendes‐Junior · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  45. Compliant Multi-electrode Micro-channel Array for Recording Afferent Nerve Activity
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  46. The Concept of Immunogenetics
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  47. Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
    Ettore Fedele, Jon H. Wetton, Mark A. Jobling · 2024 · BMC Ecology and Evolution
  48. Genome-wide regulatory effects of STRs stabilized by elevated expression of antioxidant genes in C. elegans
    Gaotian Zhang, Erik C. Andersen · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
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    Tamara Soledad Frontanilla Recalde · 2023
  50. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants
    Jinfeng Lü, Camilo Toro, David R. Adams, Undiagnosed Diseases Network, Maria T. Acosta, Margaret P Adam, Raquel L. Alvarez, Justin C. Alvey, Laura M. Amendola, Ashley Andrews et al. · 2024 · BMC Genomics
  51. Additional file 1 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi et al. · 2021 · Figshare
  52. Additional file 4 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi et al. · 2021 · Figshare
  53. Additional file 1 of STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
    Wang, Dong, Ruiyang Tao, Zhiqiang Li, Dun Pan, Zhuo Wang, Chengtao Li, Yongyong Shi · 2020 · Figshare
  54. Additional file 3 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi et al. · 2021 · Figshare
  55. Additional file 14 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Zhongzi Wu, Huanfa Gong, Zhimin Zhou, Jiang, Tao, Ziqi Lin, Jing Li, Shijun Xiao, Bin Yang, Lusheng Huang · 2022 · Figshare
  56. Additional file 5 of Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
    Chen, Hao, Yan Lü, Dongsheng Lu, Shuhua Xu · 2021 · Figshare
  57. Additional file 2 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi et al. · 2021 · Figshare
  58. Additional file 5 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi et al. · 2021 · Figshare
  59. Additional file 1 of Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
    Chen, Hao, Yan Lü, Dongsheng Lu, Shuhua Xu · 2021 · Figshare
  60. Additional file 4 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Zhongzi Wu, Huanfa Gong, Zhimin Zhou, Jiang, Tao, Ziqi Lin, Jing Li, Shijun Xiao, Bin Yang, Lusheng Huang · 2022 · Figshare
  61. Additional file 3 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Zhongzi Wu, Huanfa Gong, Zhimin Zhou, Jiang, Tao, Ziqi Lin, Jing Li, Shijun Xiao, Bin Juan Yang, Lusheng Huang · 2022 · Figshare
  62. Additional file 3 of DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing
    Fang Li, Qian Liu, Alex Mas, Pedro Gonzalez‐Alegre, Beverly L. Davidson, Kai Wang · 2022 · Figshare
  63. Additional file 4 of Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
    Hao Chen, Yan Lü, Dongsheng Lu, Shuhua Xu · 2021 · Figshare
  64. Additional file 2 of STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
    Dong Wang, Ruiyang Tao, Zhiqiang Li, Dun Pan, Zhuo Wang, Chengtao Li, Yongyong Shi · 2020 · Figshare
  65. Additional file 6 of Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
    Hao Chen, Yan Lü, Dongsheng Lu, Shuhua Xu · 2021 · Figshare
  66. Additional file 2 of DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing
    Fang Li, Qian Liu, Alex Mas, Pedro Gonzalez‐Alegre, Beverly L. Davidson, Kai Wang · 2022 · Figshare
  67. Additional file 9 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Zhongzi Wu, Huanfa Gong, Zhimin Zhou, Jiang, Tao, Ziqi Lin, Jing Li, Shijun Xiao, Bin Yang, Lusheng Huang · 2022 · Figshare
  68. Additional file 3 of STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
    Wang, Dong, Ruiyang Tao, Zhiqiang Li, Dun Pan, Zhuo Wang, Chengtao Li, Yongyong Shi · 2020 · Figshare
  69. Additional file 3 of Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
    Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu · 2021 · Figshare
  70. Genotyping Short Tandem Repeats Across Copy Number Alterations, Aneuploidies, and Polyploid Organisms
    Max Adriaan Verbiest, Elena Grassi, Andrea Bertotti, Maria O. Anisimova · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  71. StrPhaser constructs tandem repeat alleles from VCF data
    Xuewen Wang, Jonathan L. King, Huang Meng, Michael D. Coble, August E. Woerner · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  72. High short tandem repeat mutation recurrence in heat-stressed Arabidopsis thaliana lines
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  73. Bridging the Gap Between Platforms: Comparing Grape Phylloxera Daktulosphaira vitifoliae (Fitch) Microsatellite Allele Size and DNA Sequence Variation
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  78. Single Nucleotide Polymorphisms, Structural Variants, and Short Tandem Repeats Capture Distinct Signals of Adaptive Divergence in the Atlantic Puffin
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  79. A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools
    Ibra Lujumba, Yagoub Adam, Helyaneh Ziaei Jam, Itunuoluwa Isewon, Nomakhosazana Monnakgotla, Yang Li, Blessing Onyido, Kakembo Fredrick, Faith Adegoke, Jerry Emmanuel et al. · 2025 · Nature Protocols
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  83. Additional file 1 of STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci
    Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Beecroft, Sarah J., Gianina Ravenscroft, Amy J. LaCroix, Phillipa J. Lamont, Roxburgh, Richard H., Rodrigues, Miriam J. et al. · 2024 · Figshare
  84. Additional file 4 of The mutational dynamics of short tandem repeats in large, multigenerational families
    Cody J. Steely, W. Scott Watkins, Baird, Lisa, Jorde, Lynn B. · 2024 · Figshare
  85. Additional file 3 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
    Rajan-Babu, Indhu-Shree, Junran J. Peng, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Dolzhenko, Egor, Eberle, Michael A., Birol, Inanc, Friedman, Jan M. · 2021 · Figshare
  86. Additional file 5 of The mutational dynamics of short tandem repeats in large, multigenerational families
    Cody J. Steely, W. Scott Watkins, Baird, Lisa, Jorde, Lynn B. · 2024 · Figshare
  87. Additional file 7 of The mutational dynamics of short tandem repeats in large, multigenerational families
    Cody J. Steely, W. Scott Watkins, Baird, Lisa, Jorde, Lynn B. · 2024 · Figshare
  88. Additional file 4 of LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants
    Lu, Jinfeng, Toro, Camilo, David R. Adams, Moreno, Cristiane Araujo Martins, Lee, Wan-Ping, Leung, Yuk Yee, Mathew B. Harms, Badri Narayan Vardarajan, Erin L. Heinzen · 2024 · Figshare
  89. Additional file 10 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Zhang, Hongxi, Yongzhuo Fu, Zhuli Peng, Zhang, Liang, Shan Peng, Xu, Fei, Hanrou Huang, Shi, Ruixue et al. · 2021 · Figshare
  90. Additional file 1 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Wu, Zhongzi, Huanfa Gong, Zhimin Zhou, Tao Jiang, Lin, Ziqi, Li, Jing, Shijun Xiao, Yang, Bin, Huang, Lusheng · 2022 · Figshare
  91. Additional file 1 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
    Rajan-Babu, Indhu-Shree, Junran J. Peng, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Dolzhenko, Egor, Eberle, Michael A., Birol, Inanc, Jan M. Friedman · 2021 · Figshare
  92. Additional file 11 of A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Zhang, Hongxi, Yongzhuo Fu, Zhuli Peng, Zhang, Liang, Shan Peng, Xu, Fei, Hanrou Huang, Shi, Ruixue et al. · 2021 · Figshare
  93. Additional file 1 of USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences
    Wang, Xuewen, Budowle, Bruce, Jianye Ge · 2022 · Figshare
  94. Additional file 7 of Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome
    Andre L. M. Reis, Deveson, Ira W., Bindu Swapna Madala, Ted Wong, Barker, Chris, Joshua Xu, Niall J. Lennon, Tong, Weida, Tim R. Mercer · 2022 · Figshare
  95. Additional file 5 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Wu, Zhongzi, Huanfa Gong, Zhimin Zhou, Tao Jiang, Lin, Ziqi, Jing Li, Shijun Xiao, Yang, Bin, Huang, Lusheng · 2022 · Figshare
  96. Additional file 5 of LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants
    Lu, Jinfeng, Toro, Camilo, David R. Adams, Moreno, Cristiane Araujo Martins, Lee, Wan-Ping, Leung, Yuk Yee, Mathew B. Harms, Badri Narayan Vardarajan, Erin L. Heinzen · 2024 · Figshare
  97. Additional file 2 of Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses
    Kateřina Kvapilová, Pavol Mišenko, Ján Radvánszky, Ondřej Brzoň, Jaroslav Budiš, Juraj Gazdarica, Ondrej Pös, Marie Korabečná, Martin Kašný, Tomáš Szemes et al. · 2024 · Figshare
  98. Additional file 2 of LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants
    Lu, Jinfeng, Toro, Camilo, David R. Adams, Moreno, Cristiane Araujo Martins, Lee, Wan-Ping, Leung, Yuk Yee, Mathew B. Harms, Badri Narayan Vardarajan, Erin L. Heinzen · 2024 · Figshare
  99. Additional file 4 of DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing
    Fang, Li, Qian Liu, Alex Mas, Pedro Gonzalez‐Alegre, Beverly L. Davidson, Wang, Kai · 2022 · Figshare
  100. Additional file 15 of Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs
    Wu, Zhongzi, Huanfa Gong, Zhimin Zhou, Tao Jiang, Lin, Ziqi, Li, Jing, Shijun Xiao, Yang, Bin, Huang, Lusheng · 2022 · Figshare