Pavel Yakovlev Email & Phone Number

Saint Petersburg, Ru

St Petersburg City, Russia

Санкт-Петербург, Россия

From October 2014 till January 2016 the department was called Data Science, but then the title was switched to Computational Biology.Our team has more than 30 great specialists at structural and system biology, computational and medical chemistry, applied mathematics, physics and computer science. The department solves very different tasks of novel medicine development. Our primary objects of research are monoclonal antibodies, synthetic AAV-based viruses and chemical small molecules. There is a very incomplete list of solved tasks:1) antibody variable domain modeling by in-house software;2) fast GPU-based flexible protein-protein docking;3) anything-to-antibody scaffolding;4) small molecules rational design;5) machine learning-based automated retrosynthesis prediction;6) protein-protein and protein-ligand free energy calculations;7) protein aggregation and stability optimization;8) optimization of hard-to-express proteins;9) PK/PD modeling for preclinical and clinical trials;10) GPU-based NGS analysis;and so on.Since 2015 department also provide a number of production user services, like:1) YLab — a set of tools for gene synthesis design, sequencing analysis and control scripts generation for automated hardware;2) ParCur — a statistical tool for parallel curves analysis of bioassays results;3) TDS — (tool for dose selection) a software for PK/PD modeling by common models and specific effects;4) Semantic System — integrated platform for antibody structure modeling and analysis;5) LeChatelier — a recommendation system for synthesis design;and so on.At late 2016 the department switched to Haskell as a primary programming language.Since late 2017 department is also involved at general-purpose software design.Stack: Haskell, CUDA, Scala, Python, React, WebSockets, Messaging QueuesDomains: antibodies, gene therapy, small molecules design, computational physics, molecular modeling, statistical modeling, machine learning, optimization, GPGPU

Head of group up to 5 people at Molecular Biology Laboratory. The main job was to provide a service for a number of computational tasks, such as:1) high-throughput antibody variable domain sequencing processing (contigs assembly, error correction, gene extraction, clustering and annotation);2) oligonucleotides design for gene assembly by multiplex PCR;3) antibody humanization and affinity maturation;4) small molecules virtual screening and design.Stack: Scala, PythonDomains: antibody structure, combinatorial optimization, statistics, signal processing.

Санкт-Петербург, Россия

First bioinformatician at BIOCAD. Started with a couple of projects:1) automated antibody humanization algorithm;2) immune receptors sequence annotation.Stack: Python (for prototyping), C++ and ScalaDomains: Immunology, antibody structure, string algorithms, prefix structures.

ScadaStudio: the platform for Functional Controller configuration and algorithms development and debugging.Projects:1. Virtual machine for LLVM-like assembler2. Visual programming IDE (NetBeans Platform, Java)3. Visual debugger (NetBeansPlatform or Standalone, Java)4. Bay Controller configuration system

NVIDIA PhysX-based model of impact of ice on offshore structures.

Phd In Computer Science, Bioinformatics, 5.0

Master Of Science (Msc), Bioinformatics, 4.9

Bachelor Of Science (Bsc), Computer Science, 5.0

School-Leaver, Mathematics