Bioinformatics

  • dbNSFP: dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. 
  1. Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.
  2. Liu X, Jian X, and Boerwinkle E. 2013. dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Human Mutation. 34:E2393-E2402. 
  3. Liu X, Wu C, Li C and Boerwinkle E. 2016. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutation. 37(3):235-241. 
  • dbscSNV: dbscSNV includes all potential human SNVs within splicing consensus regions (−3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site), i.e. scSNVs, related functional annotations and two ensemble prediction scores for predicting their potential of altering splicing. Currently dbscSNV serves as an attached database for dbNSFP.
  1. Jian X, Boerwinkle E and Liu X. 2015. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Research 42(22):13534-13544.
  • WGSA: WGSA is an annotation pipeline for human genome re-sequencing studies, to facilitate the functional annotation step of whole genome sequencing (WGS). Currently WGSA supports the annotation of SNVs and indels locally without remote database requests, allowing it to scale up for large WGS studies.
  1. Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ and Boerwinkle E. 2016. WGSA: an annotation pipeline for human genome sequencing studies. Journal of Medical Genetics 53:111-112. 
  • dbMTS: dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study. The core functional annotations in the database are the targeting efficacy scores for the reference and mutant loci based on three microRNA target prediction algorithms, TargetScan v7.0, RNAhybrid, and miRanda. Based on their predictions, we further classify the effect of each SNV into three categories, substitution, target loss and target gain. The maximum difference between the reference score and variant-induced score was calculated to estimate how the microRNA targeting efficacy was changed after introducing the variant. Additional functional annotations of the SNVs were also collected. ​

Population Genetics

  • SRV: srv is a forward simulation algorithm, which simulates DNA sequences assuming realistic models for human demographic and natural selection. 
  1. Peng B and Liu X. 2011. Simulating Sequences of the Human Genome with Rare Variants. Human Heredity. 70(4): 287–291.
  • jPopGen Suite: jPopGen Suite is an user-friendly package of java programs for population genetic analysis of SNP spectrum data from randomly sampled DNA sequences.
  • Stairway plot: The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to hundreds of unphased sequences.
  1. Liu X and Fu YX. 2015. Exploring population size changes using SNP frequency spectra. Nature Genetics. 47(5):555-559.