Main profile profile for leszek

Research keywords: 
bioinformatics, comparative genomics, NGS, fungal pathogens

Academic qualifications and positions

Jan/2015 – onwards PostDoc in FishMed, IIMCB, Warsaw, Poland
Nov/2009 – Dec/2014 PhD in Biomedicine, Comparative Genomics, CRG, Barcelona, Spain
Oct/2008 – Sep/2009 Master training in Computational Biology, Biology Department, University of York, York, England
Oct/2007 – Jun/2008 Junior researcher in Molecular Biology, University of Huddersfield, Huddersfield, England
Oct/2004 – Jun/2007 Bachelor training in Biotechnology, Genetics Department, Silesian University, Katowice, Poland

Research visits

Dec/2016 – Dec/2016 Genome Structure & Function, Israel Institute of Technology, Haifa, Israel
Apr/2016 – Nov/2016 Computational Biology, Comenius University, Bratislava, Slovakia
Jun/2012 – Sep/2012 Genome Evolution & BioinformaticsTrinity College Dublin, Ireland
May/2009 – Sep/2009 Comparative GenomicsCRG, Barcelona, Spain

Research training

25-31 May 2013 5th FEBS Advanced Lecture Course: Human Fungal Pathogen, France
22-26 Oct 2012 Second Generation Sequencing: Lab Methods and Data Analysis; CRG, Barcelona, Spain
7-13 May 2011 4th FEBS Advanced Lecture Course: Human Fungal Pathogen 2011, La Colle sur Loup, France
5-9 Jul 2010 2nd Central European Summer Course on Mycology; Szeged, Hungary
15-19 Jun 2009 4th Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation, Valencia, Spain

I’m bioinformatician with background in molecular biology and biotechnology, fascinated by technological advancesMy principal research interest lie in creating new computational tools and applying existing ones to address molecular biology and evolutionary questions.

During my PhD thesis I was studying the evolution of virulence mechanisms in various groups of fungi, focusing on Candida clade. I’m also studying the interested in plants and microbes evolution. Recently, I’m involved in vertebrate developmental studies. Currently, I’m studying the role of RNA editing in vertebrate development

I’m an expert in NGS data analysis, including genome sequencing, RNA-Seq and ChIP-Seq. I’m keen on programming in Python and Emacs supporter in never-ending Editor war. I’m developer of metaPhOrs, the largest phylogeny-based repository of orthologs and paralogs computed from phylogenetic trees. 

In my free time, I’m keen on playing football, biking, snowboarding, ice-skating and playing chess. 

Projects I’m involved in:

  • PhylomeDB – PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). 
  • metaPhOrs – The largest repository of phylogeny-based orthologs and paralogs. 
  • Redundans – Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
  • pyScaf – Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
  • HiCembler – Assembler for HiC data. 
  • RapSi – Rapid similarity search for proteins and nucleic acids
  • REDiscover – RNA editing discovery from NGS data.
  • FastaIndex – FastA indexing and sequence retrival. 
  • tar_indexer – Random access to tar archives