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  • NAME

    Leszek Pryszcz

  • PRIMARY AFFILIATION

    IIMCB

  • SECONDARY AFFILIATION

  • DEPARTMENT #2

  • DEPARTMENT #3

  • EMAIL

  • WEBSITE #3

  • TWITTER

    Twitter:
    https://twitter.com/lpryszcz

  • OFFICE PHONE

    Office phone:

  • CELL PHONE

    Cell phone:

  • FAX

    Fax:

  • LINKEDIN

    LinkedIn:
    https://www.linkedin.com/in/leszek-pryszcz-11289747/

KEYWORDS

bioinformatics

•

genomics

•

gene regulation

•

evolution

•

development

BIO

My principal research interest lies in addressing molecular biology and evolutionary questions by applying existing computational tools. I’m keen on developing new tools as well. I’m able to fully appreciate the complexity of biological problems because of my education in biotechnology, molecular and computational biology, as well as my extensive experience in genomic research. In the course of my PhD, I was studying the emergence of virulence in various groups of fungal human pathogens. My postdoctoral research is focused more on gene regulation, addressing how post-transcriptional regulation influences expression and how it relates to changes in phenotype. Currently, I’m focused mostly on research in epitranscriptomics, its dynamics and how it affects phenotype.  

I’m expert in Python programming, fascinated by technological advances, 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), Redundans (a pipeline that assists an assembly of heterozygous/polymorphic genomes) and many other tools. 

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

KNOW-HOW

Genomics

  1. Assembly, annotation and comparative analysis of numerous newly sequenced pathogenic fungal genomes eg. Candida spp (Attila Gacser, University of Szeged, Hungary), Cryptococcus spp (Teun Boekhout, CBS, Utrecht, Netherlands).

  2. Redundans: heterozygous genome assembly pipeline: C. orthopsilosis & C. metapsilosis (Ken Wolfe, TCD, Dublin, Ireland) and Zygosaccharomyces rouxii (Lisa Solieri, University of Modena , Italy)

  3. Genomic effects of genome hybridisation (Matthias Sipiczki, University of Debrecen, Hungary)

  4. HiCembler: genome assembler from HiC data (Noam Kaplan, Technion, Haifa, Israel)

  5. pyScaf: genome scaffolder for pair-end, long reads and synteny (Tomáš Vinař, Comenius University, Bratislava, Slovakia)

Transcriptomics & Epigenomics

  1. Deciphering phenol degradation pathways in C. parapsilosis & C. albicans (Jozef Nosek, Comenius University, Bratislava, Slovakia)

  2. nextPARS: genome-wide probing of RNA secondary structures from NGS (Toni Gabaldón, CRG, Barcelona, Spain).

  3. Interactions between organisms: S. ruber (Josefa Antón, University of Alicante, Spain).

  4. REDiscover: detection of RNA editing from NGS (Mary O’Connell, CEITEC, Brno, Czechia).

  5. Transcriptomics of cucumber mosaic mitochondrial mutants (Grzegorz Bartoszewski, SGGW, Warsaw, Poland)

Phylogenomics

  1. PhylomeDB (http://phylomedb.org/): database for complete catalogs of gene phylogenies.

MetaPhOrs (http://betaorthology.phylomedb.org/): the largest database of phylogeny-based orthologs and paralogs with consistency information for each prediction.

KEY PUBLICATIONS

  1. Bizzarri M, Cassanelli S, Pryszcz LP, et al. (2018) Draft Genome Sequences of the Highly Halotolerant Strain Zygosaccharomyces rouxii ATCC 42981 and the Novel Allodiploid Strain Zygosaccharomyces sapae ATB301T Obtained Using the MinION Platform. Microbiol Resour Announc 7:e00874-18. DOI: 10.1128/MRA.00874-18

  2. Saus E, Willis JR, Pryszcz LP et al. (2018) nextPARS: Parallel probing of RNA structures in Illumina. RNA. doi: 10.1261/rna.063073.117

  3. Winata CL, Łapiński M, Pryszcz LP, et al. (2017) Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal to zygotic transition. Devel.

  4. Masgrau A, Battola A, Sanmartin T, Pryszcz LP, et al. (2017) Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast. Mol Biol Cell. 28:3082-3094

  5. Pryszcz LP and Gabaldón T. (2016) Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Res. 44:e113

  6. Altenhoff, AM, et al. (2016) Standardised Benchmarking in the Quest for Orthologs. Nature Methods. 13:425+

  7. Pryszcz LP, et al. (2015) The genomic aftermath of hybridization in the opportunistic pathogen Candida metapsilosis. PLOS Genetics, e1005626

  8. González-Torres P, Pryszcz LP, et al. (2015) Interactions between closely related bacterial strains revealed by deep transcriptome sequencing. AEM. AEM.02690-15

  9. Pryszcz LP, et al. (2014) Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol. 6:1069-78

  10. Pryszcz LP, et al. (2013) Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. Genome Biol Evol. 5: 2382-92

  11. Pryszcz LP, et al. (2011). MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res. 39: e32

“What you`re doing is rather desperate”

“You can`t always get what you want… but if you try sometimes you may get just what you need ;)”

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