Research projects

  • Epigenetic changes in aging human monocytes – a joint research project dedicated to studying healthy human aging in collaboration with Maxim Artyomov’s laboratory at Washington University in St. Louis. The group creates bioinformatics pipelines and develops novel algorithms and methods for epigenetic data analysis.
  • Immune system aging – project, which studies immune system aging in mice and humans, applying single cell methods for comprehensive characterization of cell populations' development.
  • Longitudinal analysis of human aging – study of healthy human aging, aiming to find major aging drivers using longitudinal multiomics data.

Tools

  • SPAN Peak Analyzer – is a semi-supervised multipurpose peak caller capable of processing a broad range of ChIP-seq, ATAC-seq, and single-cell ATAC-seq datasets. It robustly handles multiple replicates and noise by leveraging limited manual annotation information. SPAN is part of the semi-supervised peak calling solution.
  • JBR Genome Browser – is a fast and reliable next-generation genome browser with enhanced capabilities of viewing large sessions, semi-supervised peak and annotation functionality that is integrated with SPAN peak caller. Part of the semi-supervised peak calling solution.
  • SnakeCharm  – Snakemake workflow management system support plugin for IntelliJ Platform IDEs, adding syntax highlighting, code completion, on-the-fly code verifications and advanced integration with snakemake ecosystem.
  • Pubtrends  – is a scientific publications exploratory tool capable of analysing intellectual structure of a research field or performing analysis of similar papers. We apply bibliometrics methods to citations graphs and natural language processing algorithms to text analysis. The service allows to find most cited papers, explore topics, visualize citations and paper similarity graphs, and generate automated literature reviews.
  • Fishbone ARM – is a hybrid data mining algorithm for exploring hidden dependencies in observational datasets. It combines Associated Rules Learning technique and Information Theory for automated building of the Ishikawa diagram – a visualization method for complex patterns and rules in data.

Libraries

  • Viktor – is an open source cross-platform JNI library written in Kotlin, aimed at idiomatic multidimensional array representation and efficient vector calculations on CPU.
  • big  – BigWIG, BigBED and TDF for the JVM. BigWig and BigBED formats are data formats commonly used in bioinformatics for genomic positional data processing and visualization. The library supports both read and write operations.
  • npy – NPY and NPZ support for the JVM. NPY and NPZ are data formats introduced by NumPy - the fundamental package for scientific computing in Python. It provides a multidimensional array objects reading and writing.
  • bioinf-commons – bioinformatics library in Kotlin. Developed in the lab, bioinf-commons is general purpose bioinformatics library, used in other projects and tools like SPAN, JBR, Data mining, etc. It provides Pandas-like dataset format support for Kotlin, various APIs for working with Genome, Sequence, Genes, Ontologies objects. A dedicated statistics module contains utilities for processing various statistical distributions mixtures, Hidden Markov Models, and hypothesis testing including multiple testing corrections with Benjamini-Hocherg algorithm. Also, bioinf-commons contain various utilities like cancellable computations, progress reporters, logging utilities, and much more.

Pipelines

  • washu – reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing.
  • chipseq-smk-pipeline – technical ChIP-Seq Snakemake pipeline: from raw reads to peak calling.
  • scatac-smk-pipeline – single cell ATAC-Seq Snakemake pipeline: from raw reads to gene transcription.

Other