Research projects

  • Epigenetic changes in aging human monocytes – 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 characterizing of cell populations development.
  • Longitudinal analysis of healthy human aging - study of healthy human aging, aiming to find major aging drivers from 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 that robustly handles multiple replicates and noise by leveraging limited manual annotation information, part of semi-supervised peak calling solution.
  • JBR Genome Browser – is a fast and reliable next-generation genome browser with enhanced capabilities of view-ing large sessions, semi-supervised peak and annotation functionality that is integrated with SPAN peak caller, part of 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 research field or similar papers analysis. We apply bibliometrics method for citations information and natural language processing algorithms for text analysis. 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 from observational datasets. It combines Associated Rules Learning technique and Information Theory for automated building the Ishikawa diagram, visualization method for complex patterns and rules in your data.

Libraries

  • Viktor - is an open source Kotlin / cross-platform JNI library 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 commonly used data formats 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. Dedicated statistics module contains utilities for processing various statistical distributions mixtures, Hidden Markov Models, and hypothesis testing including multiple testing corrections by 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 - for raw reads to genes transcription

Other