ArticleGenome research2012
lobSTR: A short tandem repeat profiler for personal genomes.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
180 citing papers in PubMed, 388 citations in OpenAlex.
- Tandem repeat polymorphisms are associated with brain structure: results of two large population-based studies.Genome medicine · 2026Article
- Long-read analysis of tetrameric microsatellites with vmwhere supports GGAA repeat length-dependent chromatin state association in Ewing sarcoma.bioRxiv : the preprint server for biology · 2026Article
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- A High-Throughput Genotyping Workflow and an Optimized SSR Panel for High-Accuracy Parentage Analysis in Largemouth Black Bass.Marine biotechnology (New York, N.Y.) · 2026Article
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations.Nature communications · 2026Article
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Development and Validation of Tetranucleotide Repeat Microsatellite Markers at the Whole-Genome Level in the Yangtze Finless Porpoise.Animals : an open access journal from MDPI · 2025Article
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- Optical genome mapping enables accurate testing of large repeat expansions.Genome research · 2025Article
- Review
- Article
- A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers.Nucleic acids research · 2025Article
- ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.bioRxiv : the preprint server for biology · 2025Article
- Review
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- Genomic microsatellite characterization and development of polymorphic microsatellites in Eospalax baileyi.Scientific reports · 2025Article
- Tracking Somatic Mutations for Lineage Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression.PloS one · 2025Article
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
120 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times and a biased sampling of STR alleles. Here, we present lobSTR, a novel method for profiling STRs in personal genomes. lobSTR harnesses concepts from signal processing and statistical learning to avoid gapped alignment and to address the specific noise patterns in STR calling. The speed and reliability of lobSTR exceed the performance of current mainstream algorithms for STR profiling. We validated lobSTR's accuracy by measuring its consistency in calling STRs from whole-genome sequencing of two biological replicates from the same individual, by tracing Mendelian inheritance patterns in STR alleles in whole-genome sequencing of a HapMap trio, and by comparing lobSTR results to traditional molecular techniques. Encouraged by the speed and accuracy of lobSTR, we used the algorithm to conduct a comprehensive survey of STR variations in a deeply sequenced personal genome. We traced the mutation dynamics of close to 100,000 STR loci and observed more than 50,000 STR variations in a single genome. lobSTR's implementation is an end-to-end solution. The package accepts raw sequencing reads and provides the user with the genotyping results. It is written in C/C++, includes multi-threading capabilities, and is compatible with the BAM format.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.