For more information, please see my ORCiD or Google Scholar profile.
Preprints
Uncovering splicing-mediated disease associations in the UK Biobank and All of Us using a TWAS with Bayesian joint fine-mapping
- Alex Tokolyi, Saikat Banerjee, David A Knowles
- medRxiv, 2025. https://doi.org/10.1101/2025.09.19.25336165
SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders
- Beomjin Jang, BP Kailash, Alex Tokolyi, Winston H. Cuddleston, Ashvin Ravi, Sang-Hyuk Jung, Tatsuhiko Naito, Beomsu Kim, Min Seo Kim, Minyoung Cho, Mi-So Park, Mikaela Rosen, Joel Blanchard, Jack Humphrey, David A Knowles, Hong-Hee Won, Towfique Raj
- medRxiv, 2025. https://doi.org/10.1101/2025.03.06.25323424
Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk
- Aline Réal, BP Kailash, Winston H. Cuddleston, Benjamin Z. Muller, Beomjin Jang, Alex Tokolyi, Hong-Hee Won, Jack Humphrey, Towfique Raj, David A. Knowles
- medRxiv, 2025. https://doi.org/10.1101/2025.09.25.25336663
Published
The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes
- Alex Tokolyi, Elodie Persyn, Artika P. Nath, Katie L. Burnham, Jonathan Marten, Thomas Vanderstichele, [.. 23 more ..], Adam S. Butterworth, Michael Inouye, Emma E. Davenport, Dirk S. Paul
- Nature Genetics, 2025. https://doi.org/10.1038/s41588-025-02096-3
Phenotypic complexities of rare heterozygous neurexin-1 deletions
- Michael B. Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N. Murphy, Sarah Kammourh, P. J. Michael Deans, Sadaf Ghorbani, Ryan Onatzevitch, Adriana Pero, Christopher Padilla, Sarah E. Williams, Erin K. Flaherty, Iya A. Prytkova, Lei Cao, David A. Knowles, Gang Fang, Paul A. Slesinger & Kristen J. Brennand
- Nature, 2025. https://doi.org/10.1038/s41586-025-08864-9
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells
- Brielin C. Brown, Alex Tokolyi, John A. Morris, Tuuli Lappalainen & David A. Knowles
- Nature Communications, 2025. https://doi.org/10.1038/s41467-025-64353-7
Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk
- Omar El Garwany, Nikolaos I. Panousis, Andrew Knights, Natsuhiko Kumasaka, Maria Imaz, Lorena Boquete Vilarino, Anthi Tsingene, Alex Tokolyi, Cristina Cotobal Martin, Tobi Alegbe, Monika Krzak, Tim Raine, Alice Barnett, Celine Gomez, Daniel J. Gaffney & Carl A. Anderson
- Nature Communications, 2025. https://doi.org/10.1038/s41467-025-61669-2
Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases
- Nikolaos I. Panousis, Omar El Garwany, Andrew Knights, Jesse Cheruiyot Rop, Natsuhiko Kumasaka, Maria Imaz, Lorena Boquete Vilarino, Anthi Tsingene, Alex Tokolyi, Alice Barnett, Celine Gomez, Carl A. Anderson & Daniel J. Gaffney
- Nature Communications, 2025. https://doi.org/10.1038/s41467-025-61670-9
Variant-to-function dissection of rare non-coding GWAS loci with high impact on blood traits
- Manuel Tardaguila, Dominique Von Schiller, Michela Colombo, Ilaria Gori, Eve L Coomber, Thomas Vanderstichele, Paola Benaglio, Chiara Chiereghin, Sebastian S Gerety, Dragana Vuckovic, Arianna Landini, Giuditta Clerici, Patrick K Albers, Helen Ray-Jones, Katie L Burnham, Alex Tokolyi, Elodie Persyn, Mikhail Spivakov, Vijay G Sankaran, Klaudia Walter, Kousik Kundu, Nicola Pirastu, Michael Inouye, Dirk S Paul, Emma Davenport, Pelin Sahlen, Stephen Watt, Nicole Soranzo
- bioRxiv, 2024. https://doi.org/10.1101/2024.08.05.606572
The common, VTE-protective, G haplotype of F5 increases factor V-short, TFPI function, and risk of bleeding
- Matthew C Sims, Magdalena Gierula, Jonathan C Stephens, Alex Tokolyi, Luca Stefanucci, Elodie Persyn, Luanluan Sun, Janine H Collins, Emma E Davenport, Emanuele Di Angelantonio, Kate Downes, Michael Inouye, Dirk S Paul, Will Thomas, Alexander Tolios, NIHR BioResource, Willem H Ouwehand, Nicholas S Gleadall, James TB Crawley, Adam S Butterworth, Mattia Frontini, Josefin Ahnström
- Blood Advances, 2024. https://doi.org/10.1182/bloodadvances.2024014020
Misexpression of inactive genes in whole blood is associated with nearby rare structural variants
- Thomas Vanderstichele, Katie L Burnham, Niek de Klein, Manuel Tardaguila, Brittany Howell, Klaudia Walter, Kousik Kundu, Jonas Koeppel, Wanseon Lee,
Alex Tokolyi, Elodie Persyn, [..11 more ..], Michael Inouye, Dirk S Paul, Emma E Davenport - The American Journal of Human Genetics, 2024. https://doi.org/10.1016/j.ajhg.2024.06.017
Linear plasmids in Klebsiella and other Enterobacteriaceae
- Jane Hawkey, Hugh Cottingham, Alex Tokolyi, Ryan R. Wick, Louise M. Judd, Louise Cerdeira, Doroti de Oliveira Garcia, Kelly L. Wyres, Kathryn E. Holt
- Microbial Genomics, 2022. https://doi.org/10.1099/mgen.0.000807
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
- Youwen Qin, Aki S. Havulinna, Yang Liu, Pekka Jousilahti, Scott C. Ritchie,
Alex Tokolyi, Jon G. Sanders, Liisa Valsta, Marta Brożyńska, Qiyun Zhu, Anupriya Tripathi, Yoshiki Vazquez-Baeza, Rohit Loomba, Susan Cheng, Mohit Jain, Teemu Niiranen, Leo Lahti, Rob Knight, Veikko Salomaa, Michael Inouye, Guillaume Méric - Nature Genetics, 2022. https://doi.org/10.1038/s41588-021-00991-z
3D-Cardiomics: A spatial transcriptional atlas of the mammalian heart
- Monika Mohenska*, Nathalia M. Tan*, Alex Tokolyi*, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T. Nim, Susan K. Nilsson, David R. Powell, Nadia A. Rosenthal, Fernando J. Rossello, Mirana Ramialison, Jose M. Polo
- JMCC, 2022. https://doi.org/10.1016/j.yjmcc.2021.09.011
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
- Kelly L Wyres, Ryan R Wick, Louise M Judd, Roni Froumine, Alex Tokolyi, Claire L Gorrie, Margaret MC Lam, Sebastián Duchêne, Adam Jenney, Kathryn E Holt
- PLoS Genetics, 2019. https://doi.org/10.1371/journal.pgen.1008114
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets
- Louis T Dang, Markus Tondl, Man Ho H Chiu, Jerico Revote, Benedict Paten, Vincent Tano, Alex Tokolyi, Florence Besse, Greg Quaife-Ryan, Helen Cumming, Mark J Drvodelic, Michael P Eichenlaub, Jeannette C Hallab, Julian S Stolper, Fernando J Rossello, Marie A Bogoyevitch, David A Jans, Hieu T Nim, Enzo R Porrello, James E Hudson, Mirana Ramialison
- BMC Genomics, 2018. https://doi.org/10.1186/s12864-018-4630-0
