Dr Kathryn Crouch

Lecturer in Bioinformatics (Parasitology)

telephone: 0141 330 3746
email: Kathryn.Crouch@glasgow.ac.uk

Room B6:28, Sgdb, 120, University Place, Glasgow, G12 8TA

Biography

After finishing a PhD in Immunology at the Institute for Animal Health in 2006, I worked for four years in the pharmaceutical industry. While working on a project at Pfizer, I had the opportunity to sequence the transcriptomes of immune tissues from novel elasmobranch species (sharks) using next generation sequencing. This experience motivated me to learn more about bioinformatics, so I undertook an MSc in Bioinformatics at the University of Edinburgh.

After graduating with a distinction, I took a role as a Bioinformatician and Software Developer at the University of Glasgow. Part of this role was to provide a bioinformatics service to labs in the Wellcome Centre for Integrative Parasitology (WCIP), a position that has given me the opportunity to explore the application of computational methods to a variety of topics of importance to the parasitology community including understanding drug resistance, identifying drug targets, and exploring genome stability. As well as consolidating and extending my skills as a bioinformatician, this role has motivated me to learn more about the fascinating world of protozoan parasites.

The other part of this role was as a software developer for VEuPathDB, a genomics database for protozoan parasites, fungi and arthropod vectors. In this role, I have developed strong software development skills, but more importantly a driving interest in the provision of public resources for the research community. This was motivating by witnessing the impact that access to resources such as VEuPathDB can have, particularly on under-resourced research groups.

My vision is to use my novel combination of skills and interests to create resources enabling fair and equitable global access to public data for the purposes of data mining and hypothesis generation.

Since 2022, I have held a position as a Lecturer in Bioinformatics at the University of Glasgow, where I teach bioinformatics at undergraduate and MSc level, and retain an active role in VEuPathDB.

Research interests

My vision is to use my unique combination of software development skills and biology to create resources enabling fair and equitable global access to public data for the purposes of data mining and hypothesis generation.

Public Resources

VEuPathDB is a resource providing extensive tools for mining genome and functional genomic data for protozoan parasites, pathogenic fungi and arthropod disease vectors

MicrobiomeDB is a resource providing tools for access to and analysis of amplicon and whole-genome metagenomic data. In collaboration with Nephele, we enable users to upload their own data for analysis with our tools

Companion is a web resource enabling users to annotate a genome assembly using a high-quality reference as a template

4273pi is a resource providing free bioinformatics workshops and teacher CPD events to schools in Scotland, linked to the SQA curriculum

Publications

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Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2013 | 2012

Number of items: 25.

2024

Basenko, E. Y. et al. (2024) What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics, (doi: 10.1093/genetics/iyae035) (PMID:38529759) (Early Online Publication)

Alvarez-Jarreta, J. et al. (2024) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Research, 52(D1), D808-D816. (doi: 10.1093/nar/gkad1003) (PMID:37953350) (PMCID:PMC10767879)

2023

Bazant, W., Blevins, A. S., Crouch, K. and Beiting, D. P. (2023) Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes. Microbiome, 11, 72. (doi: 10.1186/s40168-023-01505-1) (PMID:37032329) (PMCID:PMC10084625)

Haese-Hill, W., Crouch, K. and Otto, T. D. (2023) peaks2utr: a robust Python tool for the annotation of 3’ UTRs. Bioinformatics, 39(3), btad112. (doi: 10.1093/bioinformatics/btad112) (PMID:36864613) (PMCID:PMC10008064)

Shanmugasundram, A. et al. (2023) TriTrypDB: an integrated functional genomics resource for kinetoplastida. PLoS Neglected Tropical Diseases, 17(1), e0011058. (doi: 10.1371/journal.pntd.0011058) (PMID:36656904) (PMCID:PMC9888696)

2022

Bain, S. A. , Plaisier, H., Anderson, F., Cook, N., Crouch, K. , Meagher, T. R., Ritchie, M. G., Wallace, E. W. J. and Barker, D. (2022) Bringing bioinformatics to schools with the 4273pi project. PLoS Computational Biology, 18(1), e1009705. (doi: 10.1371/journal.pcbi.1009705) (PMID:35051174) (PMCID:PMC8775354)

Amos, B. et al. (2022) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research, 50(D1), D898-D911. (doi: 10.1093/nar/gkab929) (PMID:34718728) (PMCID:PMC8728164)

2021

Steketee, P. C., Giordani, F. , Vincent, I. M. , Crouch, K. , Achcar, F. , Dickens, N. J. , Morrison, L. J., MacLeod, A. and Barrett, M. P. (2021) Transcriptional differentiation of Trypanosoma brucei during in vitro acquisition of resistance to acoziborole. PLoS Neglected Tropical Diseases, 15(11), e0009939. (doi: 10.1371/journal.pntd.0009939) (PMID:34752454) (PMCID:PMC8648117)

Steketee, P. C. et al. (2021) Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition. PLoS Pathogens, 17(7), e1009734. (doi: 10.1371/journal.ppat.1009734) (PMID:34310651) (PMCID:PMC8384185)

2020

Damasceno, J. D. , Marques, C. A. , Beraldi, D., Crouch, K. , Lapsley, C., Obonaga, R., Tosi, L. R.O. and McCulloch, R. (2020) Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife, 9, e58030. (doi: 10.7554/eLife.58030) (PMID:32897188) (PMCID:PMC7511235)

Damasceno, J. D. , Reis-Cunha, J., Crouch, K. , Beraldi, D., Lapsley, C., Tosi, L. R.O., Bartholomeu, D. and McCulloch, R. (2020) Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication. PLoS Genetics, 16(7), e1008828. (doi: 10.1371/journal.pgen.1008828) (PMID:32609721) (PMCID:PMC7360064)

Briggs, E. M., Marques, C. A., Reis-Cunha, J., Black, J., Campbell, S., Damasceno, J. , Bartholomeu, D., Crouch, K. and McCulloch, R. (2020) Next-generation analysis of trypanosomatid genome stability and instability. In: Michels, P. A.M., Ginger, M. L. and Zilberstein, D. (eds.) Trypanosomatids: Methods and Protocols. Series: Methods in Molecular Biology (2116). Springer, pp. 225-262. ISBN 9781071602935 (doi: 10.1007/978-1-0716-0294-2_15)

Black, J. A., Crouch, K. , Lemgruber, L. , Lapsley, C., Dickens, N. , Tosi, L. R.O., Mottram, J. C. and McCulloch, R. (2020) Trypanosoma brucei ATR links DNA damage signalling during antigenic variation with regulation of RNA Polymerase I-transcribed surface antigens. Cell Reports, 30(3), 836-851.e5. (doi: 10.1016/j.celrep.2019.12.049) (PMID:31968257) (PMCID:PMC6988115)

2019

Briggs, E., Crouch, K. , Lemgruber Soares, L. , Hamilton, G., Lapsley, C. and McCulloch, R. (2019) Trypanosoma brucei ribonuclease H2A is an essential R-loop processing enzyme whose loss causes DNA damage during transcription initiation and antigenic variation. Nucleic Acids Research, 47(17), pp. 9180-9197. (doi: 10.1093/nar/gkz644) (PMID:31350892) (PMCID:PMC6753483)

Alam, M. M. et al. (2019) Validation of the protein kinase PfCLK3 as a multistage cross-species malarial drug target. Science, 365(6456), eaau1682. (doi: 10.1126/science.aau1682) (PMID:31467193)

2018

Briggs, E., Hamilton, G., Crouch, K. , Lapsley, C. and McCulloch, R. (2018) Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Research, 46(22), pp. 11789-11805. (doi: 10.1093/nar/gky928) (PMID:30304482) (PMCID:PMC6294496)

Briggs, E., Crouch, K. , Lemgruber, L. , Lapsley, C. and McCulloch, R. (2018) Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. PLoS Genetics, 14(12), e1007729. (doi: 10.1371/journal.pgen.1007729) (PMID:30543624) (PMCID:PMC6292569)

Trindade, J. B. C. et al. (2018) A Leishmania infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis. EBioMedicine, 36, pp. 83-91. (doi: 10.1016/j.ebiom.2018.09.029) (PMID:30268832) (PMCID:PMC6197651)

Basenko, E. Y. et al. (2018) FungiDB: an integrated bioinformatic resource for fungi and oomycetes. Journal of Fungi, 4(1), 39. (doi: 10.3390/jof4010039) (PMID:30152809) (PMCID:PMC5872342)

Warrenfeltz, S., Basenko, E. Y., Crouch, K. , Harb, O. S., Kissinger, J. C., Roos, D. S., Shanmugasundram, A. and Silva-Franco, F. (2018) EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. In: Kollmar, M. (ed.) Eukaryotic Genomic Databases. Series: Methods in Molecular Biology, 1757. Humana Press: New York, NY, pp. 69-113. ISBN 9781493977369 (doi: 10.1007/978-1-4939-7737-6_5)

2017

Aurrecoechea, C. et al. (2017) EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Research, 45(D1), D581-D591. (doi: 10.1093/nar/gkw1105) (PMID:27903906) (PMCID:PMC5210576)

2016

Harb, O. S., Boehme, U., Crouch, K. , Ifeonu, O. O., Roos, D. S., Silva, J. C., Silva-Franco, F., Svard, S., Tretina, K. and Weedall, G. (2016) Protozoan parasite genomics. In: Walochnik, J. and Duchêne, M. (eds.) Molecular Parasitology: Genomes, Proteomes, Glycomes and Lipidomes. Springer. ISBN 9783709114162

2015

Shameer, S. et al. (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. (doi: 10.1093/nar/gku944) (PMID:25300491) (PMCID:PMC4384016)

2013

Crouch, K. , Smith, L. E., Williams, R., Cao, W., Lee, M., Jensen, A. and Dooley, H. (2013) Humoral immune response of the small-spotted catshark, Scyliorhinus canicula. Fish and Shellfish Immunology, 34(5), pp. 1158-69. (doi: 10.1016/j.fsi.2013.01.025) (PMID:23439398)

2012

Smith, L. E. et al. (2012) Characterization of the immunoglobulin repertoire of the spiny dogfish (Squalus acanthias). Developmental and Comparative Immunology, 36(4), pp. 665-679. (doi: 10.1016/j.dci.2011.10.007) (PMID:22040740)

This list was generated on Sun Apr 28 11:05:07 2024 BST.

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