Hi there :)
My name is Alex, and I am a bioinformatics professional with a doctoral degree in the field of transcriptome bioinformatics. My research project focused on disclosing the functions and evolution of lncRNAs.
I possess extensive experience in designing and implementing high-performance bioinformatics systems to store, process, harmonize, and analyze sequencing data of different modalities, such as RNA-Seq, WGS, WES, and gene panels. I am also familiar with data processing at scale using HPCs and AWS cloud infrastructure.
In industry, my work primarily revolves around designing and implementing bioinformatics solutions and data-processing pipelines, with a specific focus on gaining insights from sequencing data in the fields of cancer biology and drug discovery. My main responsibility is translating biological questions into technical tasks and designing the appropriate approach to deliver results and interpretations within a reasonable time and budget. I place a strong emphasis on achieving results.
Another area of my expertise is data analysis, including statistical analysis, exploratory data analysis (EDA), data visualization, dimensionality reduction techniques, feature engineering, and machine learning.
Work expirience
Senior Scientist II, bioinformatics
Ryvu Therapeutics, Krakow, Poland
October 2022 - current time
Senior Bioinformatician, software engineer
MNM Diagnostics, Poznan, Poland
March 2021 - September 2022
Bioinformatician, software engineer
Ideas4biology Ltd, Poznan, Poland
July 2020 - December 2020
PhD student
Adam Mickiewicz University, Poznan, Poland
April 2015 - October 2021
Bioinformatics
RNA Seq
QC, alignment,transcript assembly and quantification, differential expression analysis, differential splicing
Variant Calling
Detection of somatic or germline variants on WGS or exome sequencing data, annotation and postprocessing, CNVs, SVs, tumor only analysis
Metagenomics
Amplicon sequnce analysis as well as assembly, binning, and annotation of metagenomes.
Nextflow
Building custom pipelines, adaptation and optimization of the existing nf.core pipelines to the current needs
Bioinformatics workflows
Hard skills
Python
Pandas, numpy, scikit-learn, keras, lightgbm, plotly, matplotlib, etc.
R
Tidyverse, ggplot2, biomaRt, DESeq2, etc.
Databases
MongoDB, mariaDB, a bit of Google BigQuery
Linux
10+ years of experience, Linux advocate, Bash
Data Engineering
Nextflow, Airflow
Other
Docker, GIT, AWS (S3, EC2, Batch), Jupyter, Colab, SLURM
More about me
Soft skills
Teaching activity
Biostatistics in R
Fall 2018
course for students
Summer school of bioinformatics
Summer 2015
co-organizer
Langages
My CV and Gitlab
Hobbies
Education
Department of Integrative genomics AMU, Poznan - PhD
April 2015 - October 2021
My doctoral thesis centers on revealing connections between structure, functions and evolution of long noncoding RNAs across 11 primates and human. The project includes transcriptome assembly, identification of non-coding transcripts, prediction of orthologs, statistical analysis and database building.
Publications
DBFE: Distribution-based feature extraction from copy number and structural variants in whole-genome data (under review)
Piernik M et al.
lncEvo: automated identification and conservation study of long noncoding RNAs
Bryzghalov O, Makalowska I, Szczesniak MW.
SyntDB - defining orthologues of human long noncoding RNAs across primates.
Bryzghalov O, Szczesniak MW, Makalowska I.
CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs.
Szczesniak MW, Bryzghalov O, Ciomborowska-Basheer J, Makalowska I.
Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions.
Bryzghalov O, Szczesniak MW, Makalowska I.
Key conferences & Posters
SyntDB - a database of human lncRNA syntologs across primate species
RNA Society Meeting, Krakow, Poland
June 2019
Identification of orthologous long noncoding RNAs with transcriptomic evidence
RNA Society Meeting, Berkeley CA, USA
June 2018
Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions
SMBE 2017 Austin TX, USA
July 2017
lncRNA-RNA interactions in gene expression regulation
SMBE 2015 Vienna, Austria
July 2015
Some of attended workshops
#NGSchool2019: Machine Learning for Biomedicine, provided by #NGSchool, Poland
2019
Using interactive visualization tools to explore big data, provided by dr.Simon Anders, University of Heidelberg
2019
Tensorflow w AWS, provided by WiMLDS, Poznan
2018
Data Visualization with Circos, provided by dr.Martin Krzywinski, Genome Sciences Centre, Vancouver
2015
Contacts
