Sunyaev Lab

We develop and maintain a variety of software, genomic annotations and web services.

• Roulette is a mutation rate model identifying the mutagenic effect of Polymerase III transcription at the basepair resolution.
• Gene-based estimates of selection strength (s_het).

• PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
• SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.

• MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service and as a standalone software.

• NERINE, a network-aware rare variant association testing framework that integrates gene-gene interaction topology into a hierarchical model and aggregates human genetic variation across gene networks. It enables competitive evaluation of biological hypotheses from both canonical pathway databases and experimental screens. It can competitively select the true biological context and optimal data source for a given set of genes. It achieves higher statistical power and interpretability than traditional burden tests.
• Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
• Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
• Joint Likelihood Mapping (JLIM) 2.5 is a new version of JLIM based on summary statistics.
• scJLIM is a cluster-free colocalization test for single-cell data that links significant genetic variants from GWAS to gene expression changes by modeling eQTL interactions with continuous single-cell states. By estimateing eQTL significance and colocalization in individual cells, it improves power to detect shared genetic signals and uncovers cell-type–specific regulatory mechanisms that traditional bulk or pseudobulk approaches often miss.
• NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.
• RVTT is a novel statistical test of trend that assesses the relationship of the frequency of qualifying rare variants in a pathway with dichotomous disease phenotypes leveraging the Cochran-Armitage test statistic.

• MutPanning is designed to detect rare cancer driver genes from aggregated whole-exome sequencing data.
• CBaSE enables cancer type and gene-specific estimation of the strength of negative and positive selection. It is available as a browser-based tool as well as for download as a standalone package.

• simDoSe is a fast and flexible Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography.