Oleksandr Dudchenko

I have joined NGS team at T-Cypher Bio to perform and optimise NGS in affinity maturation screens and TCR discovery workflows. In late 2024, I have successfully set up an in-house Nanopore sequencing facility at T-Cypher. I am currently operating it on a daily basis and directly manage sample coordination, processing, downstream data analysis and results interpretation. My primary interest lies in rapid development, efficient implementation and cost-effective operation of custom, integrated wet-lab and bioinformatic workflows for various routine services (DNA QC, genotyping) and proprietary R&D projects.

With a roughly even split of my responsibilities between wet-lab and computational biology, I conducted more in-depth research in the field of promoter and enhancer discovery. In particular, I designed next iterations of synthetic promoter-enhancer libraries for screening directly in primary cells with subsequent validation in animal models. I also experimented with other molecular aspects of vector and transgene designs to further improve the regulation and specificity of transgene expression. In October 2022, I attended ESGCT conference in Edinburgh, during which I held a poster session about some of the design methodology and outcomes of hepatocyte and T cell promoter library screens. Another challenging and exciting project I worked on in this role was multiomic profiling of a proprietary rAAV producer cell line. Apart from generating RNA- and ATAC-seq Illumina libraries, I have also prepared high molecular weight genomic DNA samples for PacBio HiFi sequencing on Sequel II. With raw output from 4 flow cells exceeding 1 TB, I used sequencing data to call SNPs (DeepVariant), identify large structural re-arrangements, determine methylation status of cytosines within all CpG islands in the genome, detect nature and location of key integration sites, assemble and evaluate a haploid version of the reference genome, which was then annotated and used as a secondary reference genome for RNA- and ATAC-seq data.

I joined viral design and discovery team at OXGENE (WuXi AppTec) to establish, evaluate and optimize pipelines for high-throughput screening of tissue-specific promoter-enhancer constructs for rLV and rAAV gene therapy and biomanufacturing vectors using targeted RNA-seq and FACS-based gDNA-seq approaches. Apart from library screening, I have also been working on novel library designs based on sequence composition, transcriptomic and epigenetic data. For instance, I conducted bulk RNA-seq and ATAC-seq on multiple cell lines - from sample preparation to library generation and data analysis, as well as developed pipelines for standardized QC and processing of publicly available "omics" datasets.

As a research assistant in laboratories of selection, plant protection & seed production, I was responsible for carrying out fieldwork (setting up experimental plots, monitoring weather and soil conditions), data analysis (statistics, microscopy), international correspondence, literature search and review. During my stay at the Institute, I also attended and helped organize an International Conference on Drip Irrigation.

During my MBiolSci degree I acquired a broad range of theoretical and practical skills in biochemistry, genetics and molecular biology. Having learnt about structure-based and computer-aided drug design through literature review and in silico docking experiments, I conducted a programming project on the topic of novel intron identification in 3'-UTRs of transcripts from cancer patients. In my final year-long research project, I used bioinformatic analyses, fluorescent reporter and dual luciferase assays to investigate and annotate promoters of genes involved in differentiation, ciliogenesis and viral infection in the human airways.

A levels in Biology, Chemistry & Maths