Monika Cechova

Monika Cechova

Biography

Monika Cechova received her Ph.D. in Biology at Penn State where she studied the Y chromosome evolution in great apes, as well as applied long reads to explore heterochromatin in great apes under the supervision of prof. Kateryna Makova. She’s interested in sex chromosomes, satellite biology, non-B DNA, and reproductive biology, as well as advances in the world of long reads and assembly. Her background in computer science positions her research at the interface of biology and bioinformatics.

Interests

  • Sex Chromosomes
  • Satellite Biology and Heterochromatin
  • Long reads and complete genomes
  • Early Embryonic Development
  • Reproductive Biology

Education

  • PhD Major in Biology, Minor in Statistics, 2020

    Penn State, USA

  • MS in Bioinformatics, 2013

    Masaryk University, Brno

  • BS in Applied Informatics, 2011

    Masaryk University, Brno

Skills

R

Statistics

Python

Nanopore

3 years

PacBio

5 years

Illumina

9 years

Experience

 
 
 
 
 

Postdoc

Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University

Jun 2020 – Present Brno
  • Developing new algorithms, tools, and methods for bioinformatics
  • Gaining new understanding of the repetitive DNA
 
 
 
 
 

Postdoc

Institute of Animal Physiology and Genetics CAS, v. v. i. Central European Institute of Technology; Department of Genetics and Reproduction, Veterinary Research Institute

Mar 2020 – Dec 2020 Brno
  • Early Embryonic Development
  • Spindle Assembly Checkpoint
 
 
 
 
 

Graduate Student

Penn State

Aug 2013 – May 2020 State College, PA, USA
  • Studied driving forces of Y chromosome evolution in great apes (Cechova, Vegesna et al. 2020)
  • Explored evolution of heterochromatin in great apes (Cechova et al., 2019)
  • Characterized genome-wide effects of non-B DNA on polymerization speed and error rate (Guiblet et al., 2018)
  • Developed algorithms for the Y chromosome assembly (Rangavittal et al., 2018)
  • Characterized genes, repeats and palindromes on gorilla Y chromosome (Tomaszkiewicz, Rangavittal, Cechova et al. 2016)
  • Developed hybrid genome assembly algorithms for combining short and long reads (Tomaszkiewicz, Rangavittal, Cechova et al. 2016)
 
 
 
 
 

Bioinformatician

Institute of Biophysics, Academy of Sciences of the Czech Republic

Apr 2011 – Aug 2013 Brno
  • Developed pipelines for detection of sex-linked genes from NGS data (Cechova et al., 2015)
  • Characterized nupts and numts in 6 plant species, their age, length, distribution, consequences of insertions, etc. (Cechova et al., 2013)
  • Explored microsatellites-TEs association and microsatellite periodicity (Kejnovsky et al., 2013)

Awards

The program of support for promising postdoctoral students (PPLZ)

Mohnkern scholarship

Hill-Hill Memorial Fund Fellowship

Troxell Memorial Scholarship in Biology

CBIOS (NIH T32 Predoctoral Training Grant)

Braddock Scholarship

Best Poster Award, Genetics Conference, Lednice

Recent Publications

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Probably Correct -- Rescuing Repeats with Short and Long Reads

Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome—estimated 50–69%—is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from telomere to telomere. Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.

High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-Read Technologies

Satellite repeats are a structural component of centromeres and telomeres, and in some instances, their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups – 1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and 2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However, clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males versus females; using Y chromosome assemblies or Fluorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.

Contact

  • cechova.biomonika@gmail.com
  • Brno, Czechia 61500
  • DM Me