Curriculum 2018/20
Semester 1
  • Data Analysis in R
  • Statistics
  • Discrete Mathematics
  • Programming in Python
  • Applied Bioinformatics / Journal Club
  • Soft Skills Course
  • Project Management
  • Foreign Language in Professional Activity
  • Research Work
Semester 2
  • Systems Biology
  • Population and Medical Genetics
  • Scientific Python
  • Applied Statistics
  • High Performance Computing
  • Applied Artificial Intelligence (online)
  • Foreign Language in Professional Activity
  • Course Project
    Semester 3
    • Structural Bioinformatics
    • Metagenomics
    • Molecular Phylogenetics
    • Biotechnology
    • Applied Bioinformatics / Journal Club
    • Research Work


    Semester 4 is for Research Internship and Master's Thesis
    Syllabuses
    Statistics
    Teacher: Nikita Alexeev

    1. Probability theory: basic concepts and definitions: events, independent events, random variables
    2. Statistics: hypothesis, tests, significance, false positive and false negative errors.
    3. P-values. Null hypothesis, alternative hypothesis, significance and statistical power.
    4. Chi-square test of independence.
    5. Chi-square goodness of fit test.
    6. Tests for sample comparisons. Student's t-test and Mann-Whitney U-test.
    7. Multiple comparisons problem. Genome-wide association study. Bonferroni correction and Benjamini-Hochberg Procedure.
    8. Principal component analyses. Covariaton matrix, eigenvctors and eigenvalues.
    9. Linear regression. Simple linear regression and multiple linear regression. Analyses of missing values.
      Programming in Python
      Teacher: Dmitriy Yakutov

      1. Common syntax and basic data types
      2. More data types
      3. Modules
      4. Functions and functional programming
      5. Recursion
      6. Numpy module
      7. Classes as data types
      8. OOP basics
      Data Analysis in R
      Teacher: Valeria Bogdanova

      Introduction to R
      1. Data types and structures
      2. Program flow, functions, etc.
      3. Scoping rules, Functional approach
      4. Shiny Basics
      Data Analysis basics
      1. Data import and cleaning
      2. Data manipulation (tidyr, dplyr)
      3. Data visualization (ggplot2)
      Statistics basics
      1. Exploratory and descriptive analysis
      2. Linear Regression
      Discrete Mathematics
      Teacher: Artem Vasiliev

      1. Introduction to set theory and boolean functions
      2. Boolean logic and proof methods
      3. Combinatorics
      4. Combinatorial generation
      5. Asymptotic analysis of algorithms
      6. Sorting algorithms
      7. Dynamic programming
      8. Graph theory: basic concepts
      9. Graph theory: graph algorithms
      Systems Biology
      Systems biology overview
      Teachers: Maxim Artyomov, Alexey Sergushichev, Konstantin Zaitsev, Oleg Shpynov, Roman Chernyatchik
      1. Introduction to systems biology and immunology.
      2. Introduction to gene expression analysis. Interactive analysis in Phantasus: working with public datasets.
      3. Introduction to single cell RNA-sequencing.
      4. Introduction to epigenetics.
      5. Introduction to metabolism.

      Working with RNA-sequencing data
      Teacher: Alexey Serushichev
      1. RNA-sequencing quantification pipelines
      2. Analysis of gene expression data in R

      Proteomics

      Teacher: Pavel Sinitcyn
      1. Introduction to proteomics. Experimental protocols.
      2. Proteomics quantification.
      3. Analysis of proteomics data in Max Quant.
      4. Proteomics extras: posttranslational modifications, protein-protein interactions, spatial proteomics.
      Population and Medical Genetics
      Teacher: Mykyta Artomov

      1. Where it all started. Solving a mystery of inheritance. Mendel and post-Mendel era
      2. Pre-genome era. Mapping of the first human disease gene. Huntingnton's disease.
      3. RFPL, microsatellite and genetic linkage. Pedigree and linkage analysis. DNA forensics.
      4. Human Genome Project. SNP map of the human genome. DNA variation.
      5. Linkage disequilibrium and genome-wide association studies. HapMap project.
      6. GWAS concepts and approaches.
      7. Hands on GWAS tutorial.
      8. GWAS discussion and resources. Polygenic risk scores. UK biobank.
      9. Next generation sequencing. Exome sequencing.
      10. GATK pipeline.
      11. Variant annotations, selection pressure metrics. Large scale sequencing resources (ExAC & GnomAD).
      12. Rare variant association studies
      13. Hands-on analysis of exome sequencing data.
      14. Cancer genetics. TCGA project.
      15. Case-control matching challenge.
      Scientific Python
      Teacher: Anastasia Gainullina

      1. Regular expressions. Metacharacters, special sequences and sets. "Greedy" and "lazy" quantifiers. Lookarounds. Protein database Prosite
      2. Biopython. Bio.Data, Bio.Alphabet. Bio.Seq, Bio.SeqRecord, Bio.SeqIO. Bio.Align, Bio.Blast, Bio.Phylo. Bio.PDB
      3. Numpy, pandas, seaborn. Numpy arrays, indexing/reshaping operations, time checking. Pandas data structures, tidy data concept, data wrangling. Visualization.
      4. Error handling. Error type hierarchy. Different types of clauses. Best practices for function organization
      5. Requests. Variety of databases. Concept of API. Popular data formats. Uniprot API queries
      6. Functional programming. Iterators, generators, comprehensions. Lambdas. Partial application of functions
      7. Pipelines and OS-level virtualization.
      8. Single cell in scanpy. Common data structures and conventional pipeline. Basic data representation.
      9. Introduction to machine learning.
        Structural Bioinformatics
        Teacher: Ferdinand Molnar

        1. Defining bioinformatics and structural bioinformatics.
        2. Fundamentals of macromolecular organization and structure. Hierarchical levels of protein organization. Protein 3D structure. Protein Domains. Protein Folds.
        3. Analysis of macromolecule. Sequence and structural alignment. Amino acid substitutions, amino acid replacement matrices. Quality of protein structures, Torsion angles and Ramachadran plot. Function from structure: Structure-function relationship and analysis.
        4. Prediction and modeling of macromolecules. Homology and similarity of proteins, quality assessments of homology models. Molecular dynamics and docking, Monte Carlo simulations. Protein folding and energetics.
        5. Experimental approaches in structural biology: Determination of macromolecular structures. X-ray crystallography. Nuclear Magnetic Resonance. Cryo-electron microscopy. Hydrogen-deuterium exchange.
        6. Structure based drug design: Hit identification.
        7. Protein databases.
        Biotechnology
        Teacher: Alexander Tkachenko

        Part 1. Genetic engineering, synthetic biology. This part tells about nucleic acid manipulation methods used to create genetic constructs of different complexity.
        1. Basic genetic engineering.
        2. Gene delivery, genome editing.
        3. Gene synthesis, high-throughput cloning.
        4. Genome synthesis, synthetic signaling circuits and metabolic pathways.

        Part 2. Protein engineering, drug design. This part tells about protein and ligand design: creation of new and modification of existing proteins and small molecules.
        1. Protein design, peptide design.
        2. Antibody design, directed evolution.
        3. Ligand design, small molecule library creation and optimization.
        4. CAR-T cells.

        Part 3. Cell biotechnology, neurotechnology and neural engineering. This part tells about cell culture technology applications in biotechnology and medicine, artificial organ models, and brain-machine interfaces.
        1. Stem cells, regenerative medicine.
        2. Organoids, organ-on-a-chip, 3D bioprinting.
        3. Brain-machine interfaces, neuroprosthetics.

        Part 4. Applied biotechnology. This part tells about specific practical applications of biotechnology in industry and agriculture.
        1. Microbial biotechnology, industrial biotechnology.
        2. Plant biotechnology, agricultural biotechnology, biofuel.
        3. Biotechnology of animals, transgenic animals.
        Molecular Phylogenetics
        Teachers: Mikhail Rayko, Yury Barbitoff

        Theoretical lectures
        1. Introduction. Necessary terminology. Acquaintance with trees.
        2. Alignment of nucleotide and protein sequences.
        3. Methods for constructing phylogenetic trees: MP, ME, NJ, ML.
        4. Testing the tree topology: bootstrap, supertrees.
        5. Bayesian methods in phylogenetics. Dating
        6. Molecular Markers. Gene evolution and genome evolution.
        Practical exercises
        1. Graphical display of phylogenetic trees using R and Python.
        2. Work with NCBI databases
        3. Multiple sequence alignment tools.
        4. Cleaning the alignment. Evolution model testing.
        5. Comparison of tree reconstruction algorithms.
        6. Tree topology verification. Bootstrap analysis .
        7. Bayesian methods in phylogenetics.
        8. Discussion and debriefing.
        Metagenomics
        Part 1.
        Teacher: Ilia Korvigo

        1. A primer on linear algebra I: Algebraic structures, Vector spaces
        2. A primer on linear algebra II: Coordinate systems, Linear maps, Covariance
        3. A primer on compositional data analysis: Compositions as equivalence classes, Aitchison simplex, Principles of compositional data analysis, Generating systems on the simplex, Isomorphisms and isometries
        4. Introduction to metagenomics: Shotgun metagenomes, Amplicon libraries
        5. Taxonomic annotation: Reference databases, Alignment-based annotation, Machine learning methods, Phylogenetic placement
        6. Statistical analyses I: Diversity indices, Ordination, Location tests, Handling zeros
        7. Statistical analyses II: ILR balances, Feature selection, Mixed effects linear models
        8. Statistical analyses III: Dirichlet-multinomial regression, Logistic-normal-multinomial models

        Part 2.
        Teachers: Alexander Tyakht, Daria Kashtanova, Vera Odintsova, Natalya Klimenko

        1. Human microbiome. Analysis of 16S-data
        2. Shotgun metagenomics
        3. Clinical applications of metagenomics
        4. Statistical analysis in metagenomics
        5. Machine learning in metagenomics