About the BrykLab

Jarek Bryk

A bit about me; see also the lab expectations.

Photo of the author

PhD students

Maria Luisa Martin Cerezo (PhD 2018)

Main project: European phylogeography of Apodemus flavicolis and A. sylvaticus based on whole-genome high-density genotyping.

Marisa in the lab

Rohan Raval (PhD 2021)

Main project: Heritability of basal metabolic rates and gene regulation in torpor in a natural population of Apodemus flavicolis.

Toni Brooks, MRes/PhD student (PhD 2025)

I “inherited” Toni after her original supervisor, Dr Nik Georgopoulos, left for the Sheffield Hallam university, but we have actually worked together for a while then, as I was co-supervising Toni’s Master by Research before it turned into a PhD. Toni was working on analysis of the Dutch Scapl Cooling Registry, one of the largest datasets on clinical observations of the effects of scalp cooling on hair loss during chemotherapy. This research was supported by the Paxman Ltd and has now been published at The Oncologist, Volume 29, Issue 10, October 2024, Pages e1386–e1395.

Placement students

Alexandra Siddall (17/18)

Main project: Development and characterisation of synthetic biology constructs and protocols for use in practical educational kits. During her placement, Alex was awarded a Medical Research Scotland Vacation Scholarship and she spent 8 weeks in the lab of Dr Grzegorz Kudła in the MRC Human Genetics Unit at the University of Edinburgh, working on synthetic biology approaches to codon-usage optimisation. She was also invited (twice!) to work with Dr Jai Denton in Dr Nick Luscombe’s group at the Okinawa Institute of Science and Technology in Japan on implementation of an RNA-interference-based gene drive system in yeast.

Haeyam Tayi (19/20)

Main project: Characterisation of non-target sequences in a large RAD-seq experiment. During her placement, Haeyam was awarded The Genetics Society’s Junior Scientist Conference Grant to participate in the 53rd Population Genetics UK Group meeting in Leicester as well as the Summer Studentship, which she spent in Oxford, working with Dr Jayna Raghwani in Prof. Oliver Pybus’ group on metagenomic characterisation of viruses in wild rodents.

Lewis Ward (24/25)

Lewis’ main project is to complete and publish the maudr package (see research page), following by completing either Haeyam’s and Ray’s Kraken pipeline or getting involved in a RAD-seq data analysis project on foxes, done in collaboration with Nathan Williams and Dr Emilie Hardouin at the University of Bournemouth. In January 2024, Lewis presented his poster on maudr at the PopGroup UK 58 meeting in Sheffield, funded by the Junior Conference Grant from The Genetics Society.

Research project students

The list below mentions some of my final year research project students, who have done particularly exciting work on their projects.

  • Abbie Williams, who isolated, sequenced and put in storage a set of UNIGEMS constructs.
  • Alex Siddall, who established a SNP-based pedigree analysis pipeline based on RAD-seq data.
  • Helen Horkan, who calculated genetic distance between A. flavicollis and A. sylvaticus, based on tens of thousands of RAD-seq loci across the whole genome.
  • Haeyam Tayi, who extended Helen’s work to cover many more members of the Muridae family, and wrapped everything in a nice R script.
  • Jo Mattocks, who created the most complete and reliable list of human kinases and analysed patterns of their expression using RNA-seq data from the CCLE dataset.
  • Wayne-hon Lau (Raymond), who corrected mistakes in our code and in our biochemistry in the maudR scripts and calculated substrate limits and product inhibition of the reaction.
  • Alex Marshall, who wrote a series of R scripts to automate getting SNPs from a given genomic region from all samples in the 1000 Genomes Project and create PCA and ADMIXTURE plots for the selected populations.
  • Ophelia Forbes, who wrote an R- and Python-based pipeline to extract quantitative information on DAB staining intensity from all images in the Human Protein Atlas.

Alumni

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